flowCL report - CellA analysis
Cibi - CRCM
14 December 2015
In this document we use flowCL in order to annotate a few typical signatures. The graphical networks are in SVG format. You can view them ("View image" contextual menu) and zoom in (press Ctrl key and use mouse's wheel).
Initialize package
Let’s load the flowCL package and its dependencies.
library(flowCL)## Loading required package: Rgraphviz## Loading required package: graph## Loading required package: grid## Loading required package: SPARQL## Loading required package: XML##
## Attaching package: 'XML'## The following object is masked from 'package:graph':
##
## addNode## Loading required package: RCurl## Loading required package: bitops#flowCL("archive")
packageVersion("flowCL")## [1] '1.8.0'Here is the date of the Cell Ontology available at the queried server.
flowCL("Date")## [1] "2014-03-18 : year-month-day"We define a function that will report a standardized result
queryNReport = function(mkl, pop) {
# mkl is the queried marker pattern
# pop is the expected population name
# Do the query
system.time(Res <- flowCL(mkl, CompInfo = TRUE))
# The table from Res$Table shows many properties of the phenotype queried.
print(Res$Table)
# Plot a tree diagram helping deduction
# The cell types that contain markers are colored nodes: the green nodes are the exact matches, while the beige nodes are the partial matches. The black arrows are defined as “is a” (ex. native cell “is a” cell). The coloured arrows are the inverse of “has/lacks” some term. Each marker is associated with its own colour, which makes it easier for the user to tell which cell type contains which markers. The blue nodes are the “has” markers, while the red nodes are the “lacks” markers. The navy blue nodes are the “has” high amount markers and the grey blue nodes are the “has” low amount markers.
tmp <- Res[[mkl]]
plot(tmp[[1]], nodeAttrs=tmp[[2]], edgeAttrs=tmp[[3]], attrs=tmp[[4]], main = sprintf("Looking for %s as\n%s", pop, mkl))
# In many cases flowCL will only be used to extract the best possible cell label given a set of markers.
Res$Cell_Labels[[1]][[1]]
# All results could be formatted at once.
# Markers are displayed in the form of { A } B ( C ) [ D ]. A and B together make up the markers input for the query. B, C and D together are the markers that make up the definition of the particular cell type. C lists the markers that were part of the experiment that were not part of the query, while D lists all other markers that make up the cell type that were not part of the experimental markers. A lists all the markers in the input for the query that were not required for that particular cell type.
kable(cbind(Labels = Res$Cell_Labels[[1]], Ranking = Res$Ranking[[1]], Markers = Res$Markers[[1]]), caption = sprintf("Looking for %s as %s", pop, mkl))
}NK dim
queryNReport("CD3-CD19-CD14-CD16+CD56lo", "NK dim")## ExpMrkrLst was not defined. Defining ExpMrkrLst as MarkerList.
##
## The phenotype of interest is CD3-CD19-CD14-CD16+CD56lo
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD14 is called CD14 molecule
## Marker CD56 is called neural cell adhesion molecule 1
## The experiment phenotype of interest is CD3,CD19,CD14,CD16,CD56
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD14 is called CD14 molecule
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## Marker CD56 is called neural cell adhesion molecule 1
## Initial query results saved in
## [current directory]/flowCL_results/results/results_CD3-CD19-CD14-CD16+CD56lo.csv
## Using a cutoff score of 4
## Parent information saved in flowCL_results/parents/parent.resCD3-CD19-CD14-CD16+CD56lo.csv## Time elapsed: 00:00:00
## Iterations at 1 out of 1
##
## Total time was: 00:00:00
## Archive saved in "[current directory]/flowCL_results/"
## [,1]
## Short marker names "CD3-CD19-CD14-CD16+CD56lo"
## Ontology marker names "CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, neural cell adhesion"
## "molecule 1"
## Experiment markers "CD3,CD19,CD14,CD16,CD56"
## Ontology exper. names "CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, neural cell adhesion"
## "molecule 1"
## Successful Match? "No"
## Marker ID "1) PR_000001483, PR_000001020, PR_000001002, PR_000001889,"
## "PR_000001024"
## Marker Label "1) low affinity immunoglobulin gamma Fc region receptor III, CD3"
## "epsilon, CD19 molecule, CD14 molecule, neural cell adhesion molecule"
## "1"
## Marker Key "1) { } CD19-, CD3-, CD14-, CD16+, CD56lo ( ) [ CD20-, HLA-DR- ]"
## Score (Out of 1) "1) 0.714"
## Cell ID "1) CL_0000939"
## Cell Label "1) CD16-positive, CD56-dim natural killer cell"
| Labels | Ranking | Markers |
|---|---|---|
| CD16-positive, CD56-dim natural killer cell | 0.7142857 | { } CD19-, CD3-, CD14-, CD16+, CD56lo ( ) [ CD20-, HLA-DR- ] |
queryNReport("CD3-CD19-CD14-CD16+CD56+", "NK dim")## ExpMrkrLst was not defined. Defining ExpMrkrLst as MarkerList.
##
## The phenotype of interest is CD3-CD19-CD14-CD16+CD56+
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## Marker CD56 is called neural cell adhesion molecule 1
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD14 is called CD14 molecule
## The experiment phenotype of interest is CD3,CD19,CD14,CD16,CD56
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD14 is called CD14 molecule
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## Marker CD56 is called neural cell adhesion molecule 1
## Initial query results saved in
## [current directory]/flowCL_results/results/results_CD3-CD19-CD14-CD16+CD56+.csv
## Using a cutoff score of 3
## Parent information saved in flowCL_results/parents/parent.resCD3-CD19-CD14-CD16+CD56+.csv## Time elapsed: 00:00:01
## Iterations at 1 out of 1
##
## Total time was: 00:00:01
## Archive saved in "[current directory]/flowCL_results/"
## [,1]
## Short marker names "CD3-CD19-CD14-CD16+CD56+"
## Ontology marker names "CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, neural cell adhesion"
## "molecule 1"
## Experiment markers "CD3,CD19,CD14,CD16,CD56"
## Ontology exper. names "CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, neural cell adhesion"
## "molecule 1"
## Successful Match? "No"
## Marker ID "1) PR_000001024, PR_000001020, PR_000001002, PR_000001889 2)"
## "PR_000001020, PR_000001002, PR_000001889 3) PR_000001020,"
## "PR_000001002, PR_000001889 4) PR_000001020, PR_000001002,"
## "PR_000001889 5) PR_000001020, PR_000001002, PR_000001889 + more"
## Marker Label "1) neural cell adhesion molecule 1, CD3 epsilon, CD19 molecule, CD14"
## "molecule 2) CD3 epsilon, CD19 molecule, CD14 molecule 3) CD3 epsilon,"
## "CD19 molecule, CD14 molecule 4) CD3 epsilon, CD19 molecule, CD14"
## "molecule 5) CD3 epsilon, CD19 molecule, CD14 molecule + more"
## Marker Key "1) { CD16+ } CD19-, CD3-, CD14-, CD56+ ( ) [ CD20-, CD34 molecule-,"
## "interleukin-2 receptor subunit beta+, KLRB1-like protein+, mast/stem"
## "cell growth factor receptor+ ] 2) { CD16+, CD56+ } CD19-, CD3-, CD14-"
## "( ) [ CD20-, integrin alpha-2+, CD161c+, T-cell surface glycoprotein"
## "YE1/48+, integrin alpha-Mlo, CD27lo ] 3) { CD16+, CD56+ } CD19-,"
## "CD3-, CD14- ( ) [ CD20-, CD34 molecule+, interleukin-2 receptor"
## "subunit beta+, mast/stem cell growth factor receptor+ ] 4) { CD16+,"
## "CD56+ } CD19-, CD3-, CD14- ( ) [ CD20-, integrin alpha-Mhi, CD27hi,"
## "CD161c+ ] 5) { CD16+, CD56+ } CD19-, CD3-, CD14- ( ) [ CD20-,"
## "integrin alpha-M+, CD27+, CD161c+ ] + more"
## Score (Out of 1) "1) 0.222 2) -0.111 3) -0.143 4) -0.143 5) -0.143 + more"
## Cell ID "1) CL_0002338 2) CL_0002345 3) CL_0000937 4) CL_0002347 5) CL_0002426"
## "+ more"
## Cell Label "1) CD56-positive, CD161-positive immature natural killer cell 2)"
## "CD27-low, CD11b-low immature natural killer cell 3) pre-natural"
## "killer cell 4) CD27-high, CD11b-high natural killer cell 5)"
## "CD11b-positive, CD27-positive natural killer cell + more"
| Labels | Ranking | Markers |
|---|---|---|
| CD56-positive, CD161-positive immature natural killer cell | 0.2222222 | { CD16+ } CD19-, CD3-, CD14-, CD56+ ( ) [ CD20-, CD34 molecule-, interleukin-2 receptor subunit beta+, KLRB1-like protein+, mast/stem cell growth factor receptor+ ] |
| CD27-low, CD11b-low immature natural killer cell | -0.1111111 | { CD16+, CD56+ } CD19-, CD3-, CD14- ( ) [ CD20-, integrin alpha-2+, CD161c+, T-cell surface glycoprotein YE1/48+, integrin alpha-Mlo, CD27lo ] |
| pre-natural killer cell | -0.1428571 | { CD16+, CD56+ } CD19-, CD3-, CD14- ( ) [ CD20-, CD34 molecule+, interleukin-2 receptor subunit beta+, mast/stem cell growth factor receptor+ ] |
| CD27-high, CD11b-high natural killer cell | -0.1428571 | { CD16+, CD56+ } CD19-, CD3-, CD14- ( ) [ CD20-, integrin alpha-Mhi, CD27hi, CD161c+ ] |
| CD11b-positive, CD27-positive natural killer cell | -0.1428571 | { CD16+, CD56+ } CD19-, CD3-, CD14- ( ) [ CD20-, integrin alpha-M+, CD27+, CD161c+ ] |
queryNReport("CD3-CD19-CD14-CD16loCD56+", "NK dim")## ExpMrkrLst was not defined. Defining ExpMrkrLst as MarkerList.
##
## The phenotype of interest is CD3-CD19-CD14-CD16loCD56+
## Marker CD56 is called neural cell adhesion molecule 1
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD14 is called CD14 molecule
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## The experiment phenotype of interest is CD3,CD19,CD14,CD16,CD56
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD14 is called CD14 molecule
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## Marker CD56 is called neural cell adhesion molecule 1
## Initial query results saved in
## [current directory]/flowCL_results/results/results_CD3-CD19-CD14-CD16loCD56+.csv
## Using a cutoff score of 3
## Parent information saved in flowCL_results/parents/parent.resCD3-CD19-CD14-CD16loCD56+.csv## Time elapsed: 00:00:01
## Iterations at 1 out of 1
##
## Total time was: 00:00:01
## Archive saved in "[current directory]/flowCL_results/"
## [,1]
## Short marker names "CD3-CD19-CD14-CD16loCD56+"
## Ontology marker names "CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, neural cell adhesion"
## "molecule 1"
## Experiment markers "CD3,CD19,CD14,CD16,CD56"
## Ontology exper. names "CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, neural cell adhesion"
## "molecule 1"
## Successful Match? "No"
## Marker ID "1) PR_000001024, PR_000001020, PR_000001002, PR_000001889 2)"
## "PR_000001020, PR_000001002, PR_000001889 3) PR_000001020,"
## "PR_000001002, PR_000001889 4) PR_000001020, PR_000001002,"
## "PR_000001889 5) PR_000001020, PR_000001002, PR_000001889 + more"
## Marker Label "1) neural cell adhesion molecule 1, CD3 epsilon, CD19 molecule, CD14"
## "molecule 2) CD3 epsilon, CD19 molecule, CD14 molecule 3) CD3 epsilon,"
## "CD19 molecule, CD14 molecule 4) CD3 epsilon, CD19 molecule, CD14"
## "molecule 5) CD3 epsilon, CD19 molecule, CD14 molecule + more"
## Marker Key "1) { CD16lo } CD19-, CD3-, CD14-, CD56+ ( ) [ CD20-, CD34 molecule-,"
## "interleukin-2 receptor subunit beta+, KLRB1-like protein+, mast/stem"
## "cell growth factor receptor+ ] 2) { CD56+, CD16lo } CD19-, CD3-,"
## "CD14- ( ) [ CD20-, integrin alpha-2+, CD161c+, T-cell surface"
## "glycoprotein YE1/48+, integrin alpha-Mlo, CD27lo ] 3) { CD56+, CD16lo"
## "} CD19-, CD3-, CD14- ( ) [ CD20-, CD34 molecule+, interleukin-2"
## "receptor subunit beta+, mast/stem cell growth factor receptor+ ] 4) {"
## "CD56+, CD16lo } CD19-, CD3-, CD14- ( ) [ CD20-, integrin alpha-Mhi,"
## "CD27hi, CD161c+ ] 5) { CD56+, CD16lo } CD19-, CD3-, CD14- ( ) ["
## "CD20-, integrin alpha-M+, CD27+, CD161c+ ] + more"
## Score (Out of 1) "1) 0.222 2) -0.111 3) -0.143 4) -0.143 5) -0.143 + more"
## Cell ID "1) CL_0002338 2) CL_0002345 3) CL_0000937 4) CL_0002347 5) CL_0002426"
## "+ more"
## Cell Label "1) CD56-positive, CD161-positive immature natural killer cell 2)"
## "CD27-low, CD11b-low immature natural killer cell 3) pre-natural"
## "killer cell 4) CD27-high, CD11b-high natural killer cell 5)"
## "CD11b-positive, CD27-positive natural killer cell + more"
| Labels | Ranking | Markers |
|---|---|---|
| CD56-positive, CD161-positive immature natural killer cell | 0.2222222 | { CD16lo } CD19-, CD3-, CD14-, CD56+ ( ) [ CD20-, CD34 molecule-, interleukin-2 receptor subunit beta+, KLRB1-like protein+, mast/stem cell growth factor receptor+ ] |
| CD27-low, CD11b-low immature natural killer cell | -0.1111111 | { CD56+, CD16lo } CD19-, CD3-, CD14- ( ) [ CD20-, integrin alpha-2+, CD161c+, T-cell surface glycoprotein YE1/48+, integrin alpha-Mlo, CD27lo ] |
| pre-natural killer cell | -0.1428571 | { CD56+, CD16lo } CD19-, CD3-, CD14- ( ) [ CD20-, CD34 molecule+, interleukin-2 receptor subunit beta+, mast/stem cell growth factor receptor+ ] |
| CD27-high, CD11b-high natural killer cell | -0.1428571 | { CD56+, CD16lo } CD19-, CD3-, CD14- ( ) [ CD20-, integrin alpha-Mhi, CD27hi, CD161c+ ] |
| CD11b-positive, CD27-positive natural killer cell | -0.1428571 | { CD56+, CD16lo } CD19-, CD3-, CD14- ( ) [ CD20-, integrin alpha-M+, CD27+, CD161c+ ] |
queryNReport("CD3-CD19-CD14-CD16loCD56lo", "NK dim")## ExpMrkrLst was not defined. Defining ExpMrkrLst as MarkerList.
##
## The phenotype of interest is CD3-CD19-CD14-CD16loCD56lo
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD14 is called CD14 molecule
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## Marker CD56 is called neural cell adhesion molecule 1
## The experiment phenotype of interest is CD3,CD19,CD14,CD16,CD56
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD14 is called CD14 molecule
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## Marker CD56 is called neural cell adhesion molecule 1
## Initial query results saved in
## [current directory]/flowCL_results/results/results_CD3-CD19-CD14-CD16loCD56lo.csv
## Using a cutoff score of 3
## Parent information saved in flowCL_results/parents/parent.resCD3-CD19-CD14-CD16loCD56lo.csv## Time elapsed: 00:00:01
## Iterations at 1 out of 1
##
## Total time was: 00:00:01
## Archive saved in "[current directory]/flowCL_results/"
## [,1]
## Short marker names "CD3-CD19-CD14-CD16loCD56lo"
## Ontology marker names "CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, neural cell adhesion"
## "molecule 1"
## Experiment markers "CD3,CD19,CD14,CD16,CD56"
## Ontology exper. names "CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, neural cell adhesion"
## "molecule 1"
## Successful Match? "No"
## Marker ID "1) PR_000001020, PR_000001002, PR_000001889, PR_000001024 2)"
## "PR_000001020, PR_000001002, PR_000001889 3) PR_000001020,"
## "PR_000001002, PR_000001889 4) PR_000001020, PR_000001002,"
## "PR_000001889 5) PR_000001020, PR_000001002, PR_000001889 + more"
## Marker Label "1) CD3 epsilon, CD19 molecule, CD14 molecule, neural cell adhesion"
## "molecule 1 2) CD3 epsilon, CD19 molecule, CD14 molecule 3) CD3"
## "epsilon, CD19 molecule, CD14 molecule 4) CD3 epsilon, CD19 molecule,"
## "CD14 molecule 5) CD3 epsilon, CD19 molecule, CD14 molecule + more"
## Marker Key "1) { CD16lo } CD19-, CD3-, CD14-, CD56lo ( CD16+ ) [ CD20-, HLA-DR- ]"
## "2) { CD16lo, CD56lo } CD19-, CD3-, CD14- ( CD56+ ) [ CD20-, CD34"
## "molecule-, interleukin-2 receptor subunit beta+, KLRB1-like protein+,"
## "mast/stem cell growth factor receptor+ ] 3) { CD16lo, CD56lo } CD19-,"
## "CD3-, CD14- ( ) [ CD20-, integrin alpha-2+, CD161c+, T-cell surface"
## "glycoprotein YE1/48+, integrin alpha-Mlo, CD27lo ] 4) { CD16lo,"
## "CD56lo } CD19-, CD3-, CD14- ( ) [ CD20-, CD34 molecule+,"
## "interleukin-2 receptor subunit beta+, mast/stem cell growth factor"
## "receptor+ ] 5) { CD16lo, CD56lo } CD19-, CD3-, CD14- ( ) [ CD20-,"
## "integrin alpha-Mhi, CD27hi, CD161c+ ] + more"
## Score (Out of 1) "1) 0.286 2) -0.111 3) -0.111 4) -0.143 5) -0.143 + more"
## Cell ID "1) CL_0000939 2) CL_0002338 3) CL_0002345 4) CL_0000937 5) CL_0002347"
## "+ more"
## Cell Label "1) CD16-positive, CD56-dim natural killer cell 2) CD56-positive,"
## "CD161-positive immature natural killer cell 3) CD27-low, CD11b-low"
## "immature natural killer cell 4) pre-natural killer cell 5) CD27-high,"
## "CD11b-high natural killer cell + more"
| Labels | Ranking | Markers |
|---|---|---|
| CD16-positive, CD56-dim natural killer cell | 0.2857143 | { CD16lo } CD19-, CD3-, CD14-, CD56lo ( CD16+ ) [ CD20-, HLA-DR- ] |
| CD56-positive, CD161-positive immature natural killer cell | -0.1111111 | { CD16lo, CD56lo } CD19-, CD3-, CD14- ( CD56+ ) [ CD20-, CD34 molecule-, interleukin-2 receptor subunit beta+, KLRB1-like protein+, mast/stem cell growth factor receptor+ ] |
| CD27-low, CD11b-low immature natural killer cell | -0.1111111 | { CD16lo, CD56lo } CD19-, CD3-, CD14- ( ) [ CD20-, integrin alpha-2+, CD161c+, T-cell surface glycoprotein YE1/48+, integrin alpha-Mlo, CD27lo ] |
| pre-natural killer cell | -0.1428571 | { CD16lo, CD56lo } CD19-, CD3-, CD14- ( ) [ CD20-, CD34 molecule+, interleukin-2 receptor subunit beta+, mast/stem cell growth factor receptor+ ] |
| CD27-high, CD11b-high natural killer cell | -0.1428571 | { CD16lo, CD56lo } CD19-, CD3-, CD14- ( ) [ CD20-, integrin alpha-Mhi, CD27hi, CD161c+ ] |
queryNReport("CD3-CD19-CD14-CD16+CD56loCD33-CD123-CD1c-", "NK dim")## ExpMrkrLst was not defined. Defining ExpMrkrLst as MarkerList.
##
## The phenotype of interest is CD3-CD19-CD14-CD16+CD56loCD33-CD123-CD1c-
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD14 is called CD14 molecule
## Marker CD33 is called CD33 molecule
## Marker CD123 is called interleukin-3 receptor class 2 alpha chain
## Marker CD1c is called T-cell surface glycoprotein CD1c
## Marker CD56 is called neural cell adhesion molecule 1
## The experiment phenotype of interest is CD3,CD19,CD14,CD16,CD56,CD33,CD123,CD1c
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD14 is called CD14 molecule
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## Marker CD56 is called neural cell adhesion molecule 1
## Marker CD33 is called CD33 molecule
## Marker CD123 is called interleukin-3 receptor class 2 alpha chain
## Marker CD1c is called T-cell surface glycoprotein CD1c
## Initial query results saved in
## [current directory]/flowCL_results/results/results_CD3-CD19-CD14-CD16+CD56loCD33-CD123-CD1c-.csv
## Using a cutoff score of 4
## Parent information saved in flowCL_results/parents/parent.resCD3-CD19-CD14-CD16+CD56loCD33-CD123-CD1c-.csv## Time elapsed: 00:00:00
## Iterations at 1 out of 1
##
## Total time was: 00:00:00
## Archive saved in "[current directory]/flowCL_results/"
## [,1]
## Short marker names "CD3-CD19-CD14-CD16+CD56loCD33-CD123-CD1c-"
## Ontology marker names "CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, neural cell adhesion"
## "molecule 1, CD33 molecule, interleukin-3 receptor class 2 alpha"
## "chain, T-cell surface glycoprotein CD1c"
## Experiment markers "CD3,CD19,CD14,CD16,CD56,CD33,CD123,CD1c"
## Ontology exper. names "CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, neural cell adhesion"
## "molecule 1, CD33 molecule, interleukin-3 receptor class 2 alpha"
## "chain, T-cell surface glycoprotein CD1c"
## Successful Match? "No"
## Marker ID "1) PR_000001483, PR_000001020, PR_000001002, PR_000001889,"
## "PR_000001024"
## Marker Label "1) low affinity immunoglobulin gamma Fc region receptor III, CD3"
## "epsilon, CD19 molecule, CD14 molecule, neural cell adhesion molecule"
## "1"
## Marker Key "1) { CD33-, CD123-, CD1c- } CD19-, CD3-, CD14-, CD16+, CD56lo ( ) ["
## "CD20-, HLA-DR- ]"
## Score (Out of 1) "1) -0.143"
## Cell ID "1) CL_0000939"
## Cell Label "1) CD16-positive, CD56-dim natural killer cell"
| Labels | Ranking | Markers |
|---|---|---|
| CD16-positive, CD56-dim natural killer cell | -0.1428571 | { CD33-, CD123-, CD1c- } CD19-, CD3-, CD14-, CD16+, CD56lo ( ) [ CD20-, HLA-DR- ] |
NK bright
queryNReport("CD3-CD19-CD14-CD16-CD56hi", "NK bright")## ExpMrkrLst was not defined. Defining ExpMrkrLst as MarkerList.
##
## The phenotype of interest is CD3-CD19-CD14-CD16-CD56hi
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD14 is called CD14 molecule
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## Marker CD56 is called neural cell adhesion molecule 1
## The experiment phenotype of interest is CD3,CD19,CD14,CD16,CD56
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD14 is called CD14 molecule
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## Marker CD56 is called neural cell adhesion molecule 1
## Initial query results saved in
## [current directory]/flowCL_results/results/results_CD3-CD19-CD14-CD16-CD56hi.csv
## Using a cutoff score of 4
## Parent information saved in flowCL_results/parents/parent.resCD3-CD19-CD14-CD16-CD56hi.csv## Time elapsed: 00:00:00
## Iterations at 1 out of 1
##
## Total time was: 00:00:00
## Archive saved in "[current directory]/flowCL_results/"
## [,1]
## Short marker names "CD3-CD19-CD14-CD16-CD56hi"
## Ontology marker names "CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, neural cell adhesion"
## "molecule 1"
## Experiment markers "CD3,CD19,CD14,CD16,CD56"
## Ontology exper. names "CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, neural cell adhesion"
## "molecule 1"
## Successful Match? "No"
## Marker ID "1) PR_000001020, PR_000001002, PR_000001889, PR_000001483,"
## "PR_000001024 2) PR_000001020, PR_000001002, PR_000001889,"
## "PR_000001483, PR_000001024"
## Marker Label "1) CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, neural cell adhesion"
## "molecule 1 2) CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, neural cell adhesion"
## "molecule 1"
## Marker Key "1) { } CD19-, CD3-, CD14-, CD16-, CD56hi ( ) [ CD20-, galectin-1+ ]"
## "2) { } CD19-, CD3-, CD14-, CD16-, CD56hi ( ) [ CD20-, HLA-DR-, SLAM"
## "family member 5+ ]"
## Score (Out of 1) "1) 0.714 2) 0.625"
## Cell ID "1) CL_0002343 2) CL_0000938"
## Cell Label "1) decidual natural killer cell 2) CD16-negative, CD56-bright natural"
## "killer cell"
| Labels | Ranking | Markers |
|---|---|---|
| decidual natural killer cell | 0.7142857 | { } CD19-, CD3-, CD14-, CD16-, CD56hi ( ) [ CD20-, galectin-1+ ] |
| CD16-negative, CD56-bright natural killer cell | 0.625 | { } CD19-, CD3-, CD14-, CD16-, CD56hi ( ) [ CD20-, HLA-DR-, SLAM family member 5+ ] |
queryNReport("CD3-CD19-CD14-CD16-CD56+", "NK bright")## ExpMrkrLst was not defined. Defining ExpMrkrLst as MarkerList.
##
## The phenotype of interest is CD3-CD19-CD14-CD16-CD56+
## Marker CD56 is called neural cell adhesion molecule 1
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD14 is called CD14 molecule
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## The experiment phenotype of interest is CD3,CD19,CD14,CD16,CD56
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD14 is called CD14 molecule
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## Marker CD56 is called neural cell adhesion molecule 1
## Initial query results saved in
## [current directory]/flowCL_results/results/results_CD3-CD19-CD14-CD16-CD56+.csv
## Using a cutoff score of 3
## Parent information saved in flowCL_results/parents/parent.resCD3-CD19-CD14-CD16-CD56+.csv## Time elapsed: 00:00:01
## Iterations at 1 out of 1
##
## Total time was: 00:00:01
## Archive saved in "[current directory]/flowCL_results/"
## [,1]
## Short marker names "CD3-CD19-CD14-CD16-CD56+"
## Ontology marker names "CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, neural cell adhesion"
## "molecule 1"
## Experiment markers "CD3,CD19,CD14,CD16,CD56"
## Ontology exper. names "CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, neural cell adhesion"
## "molecule 1"
## Successful Match? "No"
## Marker ID "1) PR_000001024, PR_000001020, PR_000001002, PR_000001889 2)"
## "PR_000001020, PR_000001002, PR_000001889 3) PR_000001020,"
## "PR_000001002, PR_000001889 4) PR_000001020, PR_000001002,"
## "PR_000001889 5) PR_000001020, PR_000001002, PR_000001889 + more"
## Marker Label "1) neural cell adhesion molecule 1, CD3 epsilon, CD19 molecule, CD14"
## "molecule 2) CD3 epsilon, CD19 molecule, CD14 molecule 3) CD3 epsilon,"
## "CD19 molecule, CD14 molecule 4) CD3 epsilon, CD19 molecule, CD14"
## "molecule 5) CD3 epsilon, CD19 molecule, CD14 molecule + more"
## Marker Key "1) { CD16- } CD19-, CD3-, CD14-, CD56+ ( ) [ CD20-, CD34 molecule-,"
## "interleukin-2 receptor subunit beta+, KLRB1-like protein+, mast/stem"
## "cell growth factor receptor+ ] 2) { CD56+, CD16- } CD19-, CD3-, CD14-"
## "( ) [ CD20-, integrin alpha-2+, CD161c+, T-cell surface glycoprotein"
## "YE1/48+, integrin alpha-Mlo, CD27lo ] 3) { CD56+, CD16- } CD19-,"
## "CD3-, CD14- ( ) [ CD20-, CD34 molecule+, interleukin-2 receptor"
## "subunit beta+, mast/stem cell growth factor receptor+ ] 4) { CD56+,"
## "CD16- } CD19-, CD3-, CD14- ( ) [ CD20-, integrin alpha-Mhi, CD27hi,"
## "CD161c+ ] 5) { CD56+, CD16- } CD19-, CD3-, CD14- ( ) [ CD20-,"
## "integrin alpha-M+, CD27+, CD161c+ ] + more"
## Score (Out of 1) "1) 0.222 2) -0.111 3) -0.143 4) -0.143 5) -0.143 + more"
## Cell ID "1) CL_0002338 2) CL_0002345 3) CL_0000937 4) CL_0002347 5) CL_0002426"
## "+ more"
## Cell Label "1) CD56-positive, CD161-positive immature natural killer cell 2)"
## "CD27-low, CD11b-low immature natural killer cell 3) pre-natural"
## "killer cell 4) CD27-high, CD11b-high natural killer cell 5)"
## "CD11b-positive, CD27-positive natural killer cell + more"
| Labels | Ranking | Markers |
|---|---|---|
| CD56-positive, CD161-positive immature natural killer cell | 0.2222222 | { CD16- } CD19-, CD3-, CD14-, CD56+ ( ) [ CD20-, CD34 molecule-, interleukin-2 receptor subunit beta+, KLRB1-like protein+, mast/stem cell growth factor receptor+ ] |
| CD27-low, CD11b-low immature natural killer cell | -0.1111111 | { CD56+, CD16- } CD19-, CD3-, CD14- ( ) [ CD20-, integrin alpha-2+, CD161c+, T-cell surface glycoprotein YE1/48+, integrin alpha-Mlo, CD27lo ] |
| pre-natural killer cell | -0.1428571 | { CD56+, CD16- } CD19-, CD3-, CD14- ( ) [ CD20-, CD34 molecule+, interleukin-2 receptor subunit beta+, mast/stem cell growth factor receptor+ ] |
| CD27-high, CD11b-high natural killer cell | -0.1428571 | { CD56+, CD16- } CD19-, CD3-, CD14- ( ) [ CD20-, integrin alpha-Mhi, CD27hi, CD161c+ ] |
| CD11b-positive, CD27-positive natural killer cell | -0.1428571 | { CD56+, CD16- } CD19-, CD3-, CD14- ( ) [ CD20-, integrin alpha-M+, CD27+, CD161c+ ] |
queryNReport("CD3-CD19-CD14-CD16loCD56hi", "NK bright")## ExpMrkrLst was not defined. Defining ExpMrkrLst as MarkerList.
##
## The phenotype of interest is CD3-CD19-CD14-CD16loCD56hi
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD14 is called CD14 molecule
## Marker CD56 is called neural cell adhesion molecule 1
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## The experiment phenotype of interest is CD3,CD19,CD14,CD16,CD56
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD14 is called CD14 molecule
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## Marker CD56 is called neural cell adhesion molecule 1
## Initial query results saved in
## [current directory]/flowCL_results/results/results_CD3-CD19-CD14-CD16loCD56hi.csv
## Using a cutoff score of 3
## Parent information saved in flowCL_results/parents/parent.resCD3-CD19-CD14-CD16loCD56hi.csv## Time elapsed: 00:00:01
## Iterations at 1 out of 1
##
## Total time was: 00:00:01
## Archive saved in "[current directory]/flowCL_results/"
## [,1]
## Short marker names "CD3-CD19-CD14-CD16loCD56hi"
## Ontology marker names "CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, neural cell adhesion"
## "molecule 1"
## Experiment markers "CD3,CD19,CD14,CD16,CD56"
## Ontology exper. names "CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, neural cell adhesion"
## "molecule 1"
## Successful Match? "No"
## Marker ID "1) PR_000001020, PR_000001002, PR_000001889 2) PR_000001020,"
## "PR_000001002, PR_000001889 3) PR_000001020, PR_000001002,"
## "PR_000001889 4) PR_000001020, PR_000001002, PR_000001889 5)"
## "PR_000001020, PR_000001002, PR_000001889 + more"
## Marker Label "1) CD3 epsilon, CD19 molecule, CD14 molecule 2) CD3 epsilon, CD19"
## "molecule, CD14 molecule 3) CD3 epsilon, CD19 molecule, CD14 molecule"
## "4) CD3 epsilon, CD19 molecule, CD14 molecule 5) CD3 epsilon, CD19"
## "molecule, CD14 molecule + more"
## Marker Key "1) { CD56hi, CD16lo } CD19-, CD3-, CD14- ( CD56+ ) [ CD20-, CD34"
## "molecule-, interleukin-2 receptor subunit beta+, KLRB1-like protein+,"
## "mast/stem cell growth factor receptor+ ] 2) { CD56hi, CD16lo } CD19-,"
## "CD3-, CD14- ( ) [ CD20-, integrin alpha-2+, CD161c+, T-cell surface"
## "glycoprotein YE1/48+, integrin alpha-Mlo, CD27lo ] 3) { CD56hi,"
## "CD16lo } CD19-, CD3-, CD14- ( ) [ CD20-, CD34 molecule+,"
## "interleukin-2 receptor subunit beta+, mast/stem cell growth factor"
## "receptor+ ] 4) { CD56hi, CD16lo } CD19-, CD3-, CD14- ( ) [ CD20-,"
## "integrin alpha-Mhi, CD27hi, CD161c+ ] 5) { CD56hi, CD16lo } CD19-,"
## "CD3-, CD14- ( ) [ CD20-, integrin alpha-M+, CD27+, CD161c+ ] + more"
## Score (Out of 1) "1) -0.111 2) -0.111 3) -0.143 4) -0.143 5) -0.143 + more"
## Cell ID "1) CL_0002338 2) CL_0002345 3) CL_0000937 4) CL_0002347 5) CL_0002426"
## "+ more"
## Cell Label "1) CD56-positive, CD161-positive immature natural killer cell 2)"
## "CD27-low, CD11b-low immature natural killer cell 3) pre-natural"
## "killer cell 4) CD27-high, CD11b-high natural killer cell 5)"
## "CD11b-positive, CD27-positive natural killer cell + more"
| Labels | Ranking | Markers |
|---|---|---|
| CD56-positive, CD161-positive immature natural killer cell | -0.1111111 | { CD56hi, CD16lo } CD19-, CD3-, CD14- ( CD56+ ) [ CD20-, CD34 molecule-, interleukin-2 receptor subunit beta+, KLRB1-like protein+, mast/stem cell growth factor receptor+ ] |
| CD27-low, CD11b-low immature natural killer cell | -0.1111111 | { CD56hi, CD16lo } CD19-, CD3-, CD14- ( ) [ CD20-, integrin alpha-2+, CD161c+, T-cell surface glycoprotein YE1/48+, integrin alpha-Mlo, CD27lo ] |
| pre-natural killer cell | -0.1428571 | { CD56hi, CD16lo } CD19-, CD3-, CD14- ( ) [ CD20-, CD34 molecule+, interleukin-2 receptor subunit beta+, mast/stem cell growth factor receptor+ ] |
| CD27-high, CD11b-high natural killer cell | -0.1428571 | { CD56hi, CD16lo } CD19-, CD3-, CD14- ( ) [ CD20-, integrin alpha-Mhi, CD27hi, CD161c+ ] |
| CD11b-positive, CD27-positive natural killer cell | -0.1428571 | { CD56hi, CD16lo } CD19-, CD3-, CD14- ( ) [ CD20-, integrin alpha-M+, CD27+, CD161c+ ] |
queryNReport("CD3-CD19-CD14-CD16loCD56+", "NK bright")## ExpMrkrLst was not defined. Defining ExpMrkrLst as MarkerList.
##
## The phenotype of interest is CD3-CD19-CD14-CD16loCD56+
## Marker CD56 is called neural cell adhesion molecule 1
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD14 is called CD14 molecule
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## The experiment phenotype of interest is CD3,CD19,CD14,CD16,CD56
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD14 is called CD14 molecule
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## Marker CD56 is called neural cell adhesion molecule 1
## Initial query results saved in
## [current directory]/flowCL_results/results/results_CD3-CD19-CD14-CD16loCD56+.csv
## Using a cutoff score of 3
## Parent information saved in flowCL_results/parents/parent.resCD3-CD19-CD14-CD16loCD56+.csv## Time elapsed: 00:00:01
## Iterations at 1 out of 1
##
## Total time was: 00:00:01
## Archive saved in "[current directory]/flowCL_results/"
## [,1]
## Short marker names "CD3-CD19-CD14-CD16loCD56+"
## Ontology marker names "CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, neural cell adhesion"
## "molecule 1"
## Experiment markers "CD3,CD19,CD14,CD16,CD56"
## Ontology exper. names "CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, neural cell adhesion"
## "molecule 1"
## Successful Match? "No"
## Marker ID "1) PR_000001024, PR_000001020, PR_000001002, PR_000001889 2)"
## "PR_000001020, PR_000001002, PR_000001889 3) PR_000001020,"
## "PR_000001002, PR_000001889 4) PR_000001020, PR_000001002,"
## "PR_000001889 5) PR_000001020, PR_000001002, PR_000001889 + more"
## Marker Label "1) neural cell adhesion molecule 1, CD3 epsilon, CD19 molecule, CD14"
## "molecule 2) CD3 epsilon, CD19 molecule, CD14 molecule 3) CD3 epsilon,"
## "CD19 molecule, CD14 molecule 4) CD3 epsilon, CD19 molecule, CD14"
## "molecule 5) CD3 epsilon, CD19 molecule, CD14 molecule + more"
## Marker Key "1) { CD16lo } CD19-, CD3-, CD14-, CD56+ ( ) [ CD20-, CD34 molecule-,"
## "interleukin-2 receptor subunit beta+, KLRB1-like protein+, mast/stem"
## "cell growth factor receptor+ ] 2) { CD56+, CD16lo } CD19-, CD3-,"
## "CD14- ( ) [ CD20-, integrin alpha-2+, CD161c+, T-cell surface"
## "glycoprotein YE1/48+, integrin alpha-Mlo, CD27lo ] 3) { CD56+, CD16lo"
## "} CD19-, CD3-, CD14- ( ) [ CD20-, CD34 molecule+, interleukin-2"
## "receptor subunit beta+, mast/stem cell growth factor receptor+ ] 4) {"
## "CD56+, CD16lo } CD19-, CD3-, CD14- ( ) [ CD20-, integrin alpha-Mhi,"
## "CD27hi, CD161c+ ] 5) { CD56+, CD16lo } CD19-, CD3-, CD14- ( ) ["
## "CD20-, integrin alpha-M+, CD27+, CD161c+ ] + more"
## Score (Out of 1) "1) 0.222 2) -0.111 3) -0.143 4) -0.143 5) -0.143 + more"
## Cell ID "1) CL_0002338 2) CL_0002345 3) CL_0000937 4) CL_0002347 5) CL_0002426"
## "+ more"
## Cell Label "1) CD56-positive, CD161-positive immature natural killer cell 2)"
## "CD27-low, CD11b-low immature natural killer cell 3) pre-natural"
## "killer cell 4) CD27-high, CD11b-high natural killer cell 5)"
## "CD11b-positive, CD27-positive natural killer cell + more"
| Labels | Ranking | Markers |
|---|---|---|
| CD56-positive, CD161-positive immature natural killer cell | 0.2222222 | { CD16lo } CD19-, CD3-, CD14-, CD56+ ( ) [ CD20-, CD34 molecule-, interleukin-2 receptor subunit beta+, KLRB1-like protein+, mast/stem cell growth factor receptor+ ] |
| CD27-low, CD11b-low immature natural killer cell | -0.1111111 | { CD56+, CD16lo } CD19-, CD3-, CD14- ( ) [ CD20-, integrin alpha-2+, CD161c+, T-cell surface glycoprotein YE1/48+, integrin alpha-Mlo, CD27lo ] |
| pre-natural killer cell | -0.1428571 | { CD56+, CD16lo } CD19-, CD3-, CD14- ( ) [ CD20-, CD34 molecule+, interleukin-2 receptor subunit beta+, mast/stem cell growth factor receptor+ ] |
| CD27-high, CD11b-high natural killer cell | -0.1428571 | { CD56+, CD16lo } CD19-, CD3-, CD14- ( ) [ CD20-, integrin alpha-Mhi, CD27hi, CD161c+ ] |
| CD11b-positive, CD27-positive natural killer cell | -0.1428571 | { CD56+, CD16lo } CD19-, CD3-, CD14- ( ) [ CD20-, integrin alpha-M+, CD27+, CD161c+ ] |
queryNReport("CD3-CD19-CD14-CD16-CD56hiCD33-CD123-CD1c-", "NK bright")## ExpMrkrLst was not defined. Defining ExpMrkrLst as MarkerList.
##
## The phenotype of interest is CD3-CD19-CD14-CD16-CD56hiCD33-CD123-CD1c-
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD14 is called CD14 molecule
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## Marker CD33 is called CD33 molecule
## Marker CD123 is called interleukin-3 receptor class 2 alpha chain
## Marker CD1c is called T-cell surface glycoprotein CD1c
## Marker CD56 is called neural cell adhesion molecule 1
## The experiment phenotype of interest is CD3,CD19,CD14,CD16,CD56,CD33,CD123,CD1c
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD14 is called CD14 molecule
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## Marker CD56 is called neural cell adhesion molecule 1
## Marker CD33 is called CD33 molecule
## Marker CD123 is called interleukin-3 receptor class 2 alpha chain
## Marker CD1c is called T-cell surface glycoprotein CD1c
## Initial query results saved in
## [current directory]/flowCL_results/results/results_CD3-CD19-CD14-CD16-CD56hiCD33-CD123-CD1c-.csv
## Using a cutoff score of 4
## Parent information saved in flowCL_results/parents/parent.resCD3-CD19-CD14-CD16-CD56hiCD33-CD123-CD1c-.csv## Time elapsed: 00:00:00
## Iterations at 1 out of 1
##
## Total time was: 00:00:00
## Archive saved in "[current directory]/flowCL_results/"
## [,1]
## Short marker names "CD3-CD19-CD14-CD16-CD56hiCD33-CD123-CD1c-"
## Ontology marker names "CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, neural cell adhesion"
## "molecule 1, CD33 molecule, interleukin-3 receptor class 2 alpha"
## "chain, T-cell surface glycoprotein CD1c"
## Experiment markers "CD3,CD19,CD14,CD16,CD56,CD33,CD123,CD1c"
## Ontology exper. names "CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, neural cell adhesion"
## "molecule 1, CD33 molecule, interleukin-3 receptor class 2 alpha"
## "chain, T-cell surface glycoprotein CD1c"
## Successful Match? "No"
## Marker ID "1) PR_000001020, PR_000001002, PR_000001889, PR_000001483,"
## "PR_000001024 2) PR_000001020, PR_000001002, PR_000001889,"
## "PR_000001483, PR_000001024"
## Marker Label "1) CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, neural cell adhesion"
## "molecule 1 2) CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, neural cell adhesion"
## "molecule 1"
## Marker Key "1) { CD33-, CD123-, CD1c- } CD19-, CD3-, CD14-, CD16-, CD56hi ( ) ["
## "CD20-, HLA-DR-, SLAM family member 5+ ] 2) { CD33-, CD123-, CD1c- }"
## "CD19-, CD3-, CD14-, CD16-, CD56hi ( ) [ CD20-, galectin-1+ ]"
## Score (Out of 1) "1) -0.125 2) -0.143"
## Cell ID "1) CL_0000938 2) CL_0002343"
## Cell Label "1) CD16-negative, CD56-bright natural killer cell 2) decidual natural"
## "killer cell"
| Labels | Ranking | Markers |
|---|---|---|
| CD16-negative, CD56-bright natural killer cell | -0.125 | { CD33-, CD123-, CD1c- } CD19-, CD3-, CD14-, CD16-, CD56hi ( ) [ CD20-, HLA-DR-, SLAM family member 5+ ] |
| decidual natural killer cell | -0.1428571 | { CD33-, CD123-, CD1c- } CD19-, CD3-, CD14-, CD16-, CD56hi ( ) [ CD20-, galectin-1+ ] |
Monocytes
mkl <- "CD56-CD16-CD14+CD33+CD123-CD1c-"
queryNReport("CD3-CD19-CD14+CD16-CD33+", "Monocytes")## ExpMrkrLst was not defined. Defining ExpMrkrLst as MarkerList.
##
## The phenotype of interest is CD3-CD19-CD14+CD16-CD33+
## Marker CD14 is called CD14 molecule
## Marker CD33 is called CD33 molecule
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## The experiment phenotype of interest is CD3,CD19,CD14,CD16,CD33
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD14 is called CD14 molecule
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## Marker CD33 is called CD33 molecule
## Initial query results saved in
## [current directory]/flowCL_results/results/results_CD3-CD19-CD14+CD16-CD33+.csv
## Using a cutoff score of 3
## Parent information saved in flowCL_results/parents/parent.resCD3-CD19-CD14+CD16-CD33+.csv## Time elapsed: 00:00:01
## Iterations at 1 out of 1
##
## Total time was: 00:00:01
## Archive saved in "[current directory]/flowCL_results/"
## [,1]
## Short marker names "CD3-CD19-CD14+CD16-CD33+"
## Ontology marker names "CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, CD33 molecule"
## Experiment markers "CD3,CD19,CD14,CD16,CD33"
## Ontology exper. names "CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, CD33 molecule"
## Successful Match? "No"
## Marker ID "1) PR_000001889, PR_000001020, PR_000001002, PR_000001483 2)"
## "PR_000001892, PR_000001020, PR_000001002, PR_000001483 3)"
## "PR_000001892, PR_000001020, PR_000001002, PR_000001483 4)"
## "PR_000001892, PR_000001020, PR_000001002, PR_000001483 5)"
## "PR_000001889, PR_000001020, PR_000001002 + more"
## Marker Label "1) CD14 molecule, CD3 epsilon, CD19 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III 2) CD33 molecule, CD3"
## "epsilon, CD19 molecule, low affinity immunoglobulin gamma Fc region"
## "receptor III 3) CD33 molecule, CD3 epsilon, CD19 molecule, low"
## "affinity immunoglobulin gamma Fc region receptor III 4) CD33"
## "molecule, CD3 epsilon, CD19 molecule, low affinity immunoglobulin"
## "gamma Fc region receptor III 5) CD14 molecule, CD3 epsilon, CD19"
## "molecule + more"
## Marker Key "1) { CD33+ } CD19-, CD3-, CD16-, CD14+ ( ) [ CD20-, high affinity"
## "immunoglobulin gamma Fc receptor I+, scavenger receptor cysteine-rich"
## "type 1 protein M130+, CX3C chemokine receptor 1lo, C-C chemokine"
## "receptor type 2hi ] 2) { CD14+ } CD19-, CD3-, CD16-, CD33+ ( ) ["
## "CD56-, T-cell surface glycoprotein CD8 alpha chain-, integrin"
## "alpha-M+, carcinoembryonic antigen-related cell adhesion molecule 8+,"
## "urokinase plasminogen activator surface receptor+,"
## "alpha-(1,3)-fucosyltransferase FUT4, signal transducer CD24+,"
## "aminopeptidase N+, low affinity immunoglobulin gamma Fc region"
## "receptor II+, leukosialin+ ] 3) { CD14+ } CD19-, CD3-, CD16-, CD33+ ("
## ") [ CD56-, T-cell surface glycoprotein CD8 alpha chain-, integrin"
## "alpha-M+, carcinoembryonic antigen-related cell adhesion molecule 8+,"
## "urokinase plasminogen activator surface receptor+,"
## "alpha-(1,3)-fucosyltransferase FUT4, signal transducer CD24+,"
## "aminopeptidase N+, chemokine receptor CCR1+, chemokine receptor"
## "CCR3+, CD44 molecule+, CD69 molecule+, CD9 molecule+ ] 4) { CD14+ }"
## "CD19-, CD3-, CD16-, CD33+ ( ) [ CD56-, T-cell surface glycoprotein"
## "CD8 alpha chain-, integrin alpha-M+, carcinoembryonic antigen-related"
## "cell adhesion molecule 8+, urokinase plasminogen activator surface"
## "receptor+, alpha-(1,3)-fucosyltransferase FUT4, signal transducer"
## "CD24+, aminopeptidase N+, ectonucleotide"
## "pyrophosphatase/phosphodiesterase family member 3+, tumor necrosis"
## "factor ligand superfamily member 5+, chemokine receptor CCR3hi,"
## "CD123hi, high affinity immunoglobulin epsilon receptor subunit"
## "alphahi ] 5) { CD33+, CD16- } CD19-, CD3-, CD14+ ( ) [ CD34"
## "molecule-, CD56-, CD20-, T-cell surface glycoprotein CD1a-, CD83"
## "molecule+, integrin alpha-M+, lymphocyte antigen 75+, T-cell surface"
## "glycoprotein CD8 alpha chain+, MHC class II protein complexhi, CD86"
## "moleculehi, CD80 moleculehi, integrin alpha-Xhi ] + more"
## Score (Out of 1) "1) 0.222 2) 0.143 3) 0.118 4) 0.118 5) -0.067 + more"
## Cell ID "1) CL_0002057 2) CL_0000580 3) CL_0000612 4) CL_0000614 5) CL_0002528"
## "+ more"
## Cell Label "1) CD14-positive, CD16-negative classical monocyte 2) neutrophilic"
## "myelocyte 3) eosinophilic myelocyte 4) basophilic myelocyte 5) mature"
## "CD14-positive dermal dendritic cell + more"
| Labels | Ranking | Markers |
|---|---|---|
| CD14-positive, CD16-negative classical monocyte | 0.2222222 | { CD33+ } CD19-, CD3-, CD16-, CD14+ ( ) [ CD20-, high affinity immunoglobulin gamma Fc receptor I+, scavenger receptor cysteine-rich type 1 protein M130+, CX3C chemokine receptor 1lo, C-C chemokine receptor type 2hi ] |
| neutrophilic myelocyte | 0.1428571 | { CD14+ } CD19-, CD3-, CD16-, CD33+ ( ) [ CD56-, T-cell surface glycoprotein CD8 alpha chain-, integrin alpha-M+, carcinoembryonic antigen-related cell adhesion molecule 8+, urokinase plasminogen activator surface receptor+, alpha-(1,3)-fucosyltransferase FUT4, signal transducer CD24+, aminopeptidase N+, low affinity immunoglobulin gamma Fc region receptor II+, leukosialin+ ] |
| eosinophilic myelocyte | 0.1176471 | { CD14+ } CD19-, CD3-, CD16-, CD33+ ( ) [ CD56-, T-cell surface glycoprotein CD8 alpha chain-, integrin alpha-M+, carcinoembryonic antigen-related cell adhesion molecule 8+, urokinase plasminogen activator surface receptor+, alpha-(1,3)-fucosyltransferase FUT4, signal transducer CD24+, aminopeptidase N+, chemokine receptor CCR1+, chemokine receptor CCR3+, CD44 molecule+, CD69 molecule+, CD9 molecule+ ] |
| basophilic myelocyte | 0.1176471 | { CD14+ } CD19-, CD3-, CD16-, CD33+ ( ) [ CD56-, T-cell surface glycoprotein CD8 alpha chain-, integrin alpha-M+, carcinoembryonic antigen-related cell adhesion molecule 8+, urokinase plasminogen activator surface receptor+, alpha-(1,3)-fucosyltransferase FUT4, signal transducer CD24+, aminopeptidase N+, ectonucleotide pyrophosphatase/phosphodiesterase family member 3+, tumor necrosis factor ligand superfamily member 5+, chemokine receptor CCR3hi, CD123hi, high affinity immunoglobulin epsilon receptor subunit alphahi ] |
| mature CD14-positive dermal dendritic cell | -0.06666667 | { CD33+, CD16- } CD19-, CD3-, CD14+ ( ) [ CD34 molecule-, CD56-, CD20-, T-cell surface glycoprotein CD1a-, CD83 molecule+, integrin alpha-M+, lymphocyte antigen 75+, T-cell surface glycoprotein CD8 alpha chain+, MHC class II protein complexhi, CD86 moleculehi, CD80 moleculehi, integrin alpha-Xhi ] |
queryNReport("CD3-CD19-CD14+CD16-", "Monocytes")## ExpMrkrLst was not defined. Defining ExpMrkrLst as MarkerList.
##
## The phenotype of interest is CD3-CD19-CD14+CD16-
## Marker CD14 is called CD14 molecule
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## The experiment phenotype of interest is CD3,CD19,CD14,CD16
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD14 is called CD14 molecule
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## Initial query results saved in
## [current directory]/flowCL_results/results/results_CD3-CD19-CD14+CD16-.csv
## Using a cutoff score of 3
## Parent information saved in flowCL_results/parents/parent.resCD3-CD19-CD14+CD16-.csv## Time elapsed: 00:00:00
## Iterations at 1 out of 1
##
## Total time was: 00:00:00
## Archive saved in "[current directory]/flowCL_results/"
## [,1]
## Short marker names "CD3-CD19-CD14+CD16-"
## Ontology marker names "CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III"
## Experiment markers "CD3,CD19,CD14,CD16"
## Ontology exper. names "CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III"
## Successful Match? "No"
## Marker ID "1) PR_000001889, PR_000001020, PR_000001002, PR_000001483 2)"
## "PR_000001889, PR_000001020, PR_000001002 3) PR_000001889,"
## "PR_000001020, PR_000001002 4) PR_000001889, PR_000001020,"
## "PR_000001002 5) PR_000001020, PR_000001002, PR_000001483 + more"
## Marker Label "1) CD14 molecule, CD3 epsilon, CD19 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III 2) CD14 molecule, CD3"
## "epsilon, CD19 molecule 3) CD14 molecule, CD3 epsilon, CD19 molecule"
## "4) CD14 molecule, CD3 epsilon, CD19 molecule 5) CD3 epsilon, CD19"
## "molecule, low affinity immunoglobulin gamma Fc region receptor III +"
## "more"
## Marker Key "1) { } CD19-, CD3-, CD16-, CD14+ ( ) [ CD20-, high affinity"
## "immunoglobulin gamma Fc receptor I+, scavenger receptor cysteine-rich"
## "type 1 protein M130+, CX3C chemokine receptor 1lo, C-C chemokine"
## "receptor type 2hi ] 2) { CD16- } CD19-, CD3-, CD14+ ( ) [ CD20- ] 3)"
## "{ CD16- } CD19-, CD3-, CD14+ ( ) [ CD34 molecule-, CD56-, CD20-,"
## "T-cell surface glycoprotein CD1a-, integrin alpha-M+, lymphocyte"
## "antigen 75+, T-cell surface glycoprotein CD8 alpha chain+, integrin"
## "alpha-Xhi ] 4) { CD16- } CD19-, CD3-, CD14+ ( ) [ CD34 molecule-,"
## "CD56-, CD20-, T-cell surface glycoprotein CD1a-, integrin alpha-M+,"
## "lymphocyte antigen 75+, T-cell surface glycoprotein CD8 alpha chain+,"
## "MHC class II protein complexlo, CD86 moleculelo, CD80 moleculelo,"
## "integrin alpha-Xhi ] 5) { CD14+ } CD19-, CD3-, CD16- ( ) [ CD56-,"
## "T-cell surface glycoprotein CD8 alpha chain-, integrin alpha-M+,"
## "carcinoembryonic antigen-related cell adhesion molecule 8+, urokinase"
## "plasminogen activator surface receptor+,"
## "alpha-(1,3)-fucosyltransferase FUT4, CD33+, signal transducer CD24+,"
## "aminopeptidase N+, low affinity immunoglobulin gamma Fc region"
## "receptor II+, leukosialin+ ] + more"
## Score (Out of 1) "1) 0.444 2) 0.25 3) 0.091 4) 0.071 5) 0.071 + more"
## Cell ID "1) CL_0002057 2) CL_0001054 3) CL_0002526 4) CL_0002527 5) CL_0000580"
## "+ more"
## Cell Label "1) CD14-positive, CD16-negative classical monocyte 2) CD14-positive"
## "monocyte 3) CD14-positive dermal dendritic cell 4) immature"
## "CD14-positive dermal dendritic cell 5) neutrophilic myelocyte + more"
| Labels | Ranking | Markers |
|---|---|---|
| CD14-positive, CD16-negative classical monocyte | 0.4444444 | { } CD19-, CD3-, CD16-, CD14+ ( ) [ CD20-, high affinity immunoglobulin gamma Fc receptor I+, scavenger receptor cysteine-rich type 1 protein M130+, CX3C chemokine receptor 1lo, C-C chemokine receptor type 2hi ] |
| CD14-positive monocyte | 0.25 | { CD16- } CD19-, CD3-, CD14+ ( ) [ CD20- ] |
| CD14-positive dermal dendritic cell | 0.09090909 | { CD16- } CD19-, CD3-, CD14+ ( ) [ CD34 molecule-, CD56-, CD20-, T-cell surface glycoprotein CD1a-, integrin alpha-M+, lymphocyte antigen 75+, T-cell surface glycoprotein CD8 alpha chain+, integrin alpha-Xhi ] |
| immature CD14-positive dermal dendritic cell | 0.07142857 | { CD16- } CD19-, CD3-, CD14+ ( ) [ CD34 molecule-, CD56-, CD20-, T-cell surface glycoprotein CD1a-, integrin alpha-M+, lymphocyte antigen 75+, T-cell surface glycoprotein CD8 alpha chain+, MHC class II protein complexlo, CD86 moleculelo, CD80 moleculelo, integrin alpha-Xhi ] |
| neutrophilic myelocyte | 0.07142857 | { CD14+ } CD19-, CD3-, CD16- ( ) [ CD56-, T-cell surface glycoprotein CD8 alpha chain-, integrin alpha-M+, carcinoembryonic antigen-related cell adhesion molecule 8+, urokinase plasminogen activator surface receptor+, alpha-(1,3)-fucosyltransferase FUT4, CD33+, signal transducer CD24+, aminopeptidase N+, low affinity immunoglobulin gamma Fc region receptor II+, leukosialin+ ] |
queryNReport("CD3-CD19-CD14+", "Monocytes")## ExpMrkrLst was not defined. Defining ExpMrkrLst as MarkerList.
##
## The phenotype of interest is CD3-CD19-CD14+
## Marker CD14 is called CD14 molecule
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## The experiment phenotype of interest is CD3,CD19,CD14
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD14 is called CD14 molecule
## Initial query results saved in
## [current directory]/flowCL_results/results/results_CD3-CD19-CD14+.csv
## Using a cutoff score of 3
## Parent information saved in flowCL_results/parents/parent.resCD3-CD19-CD14+.csv## Time elapsed: 00:00:00
## Iterations at 1 out of 1
##
## Total time was: 00:00:00
## Archive saved in "[current directory]/flowCL_results/"
## [,1]
## Short marker names "CD3-CD19-CD14+"
## Ontology marker names "CD3 epsilon, CD19 molecule, CD14 molecule"
## Experiment markers "CD3,CD19,CD14"
## Ontology exper. names "CD3 epsilon, CD19 molecule, CD14 molecule"
## Successful Match? "No"
## Marker ID "1) PR_000001889, PR_000001020, PR_000001002 2) PR_000001889,"
## "PR_000001020, PR_000001002 3) PR_000001889, PR_000001020,"
## "PR_000001002 4) PR_000001889, PR_000001020, PR_000001002 5)"
## "PR_000001889, PR_000001020, PR_000001002 + more"
## Marker Label "1) CD14 molecule, CD3 epsilon, CD19 molecule 2) CD14 molecule, CD3"
## "epsilon, CD19 molecule 3) CD14 molecule, CD3 epsilon, CD19 molecule"
## "4) CD14 molecule, CD3 epsilon, CD19 molecule 5) CD14 molecule, CD3"
## "epsilon, CD19 molecule + more"
## Marker Key "1) { } CD19-, CD3-, CD14+ ( ) [ CD20- ] 2) { } CD19-, CD3-, CD14+ ( )"
## "[ CD20-, C-C chemokine receptor type 2-, CD16lo ] 3) { } CD19-, CD3-,"
## "CD14+ ( ) [ CD20-, C-C chemokine receptor type 2-, CD16+ ] 4) { }"
## "CD19-, CD3-, CD14+ ( ) [ C-C chemokine receptor type 2-, CD20-,"
## "CD16+, CX3C chemokine receptor 1hi ] 5) { } CD19-, CD3-, CD14+ ( ) ["
## "CD20-, CD16-, high affinity immunoglobulin gamma Fc receptor I+,"
## "scavenger receptor cysteine-rich type 1 protein M130+, CX3C chemokine"
## "receptor 1lo, C-C chemokine receptor type 2hi ] + more"
## Score (Out of 1) "1) 0.75 2) 0.5 3) 0.5 4) 0.429 5) 0.333 + more"
## Cell ID "1) CL_0001054 2) CL_0001055 3) CL_0002397 4) CL_0002396 5) CL_0002057"
## "+ more"
## Cell Label "1) CD14-positive monocyte 2) CD14-positive, CD16-low monocyte 3)"
## "CD14-positive, CD16-positive monocyte 4) CD14-low, CD16-positive"
## "monocyte 5) CD14-positive, CD16-negative classical monocyte + more"
| Labels | Ranking | Markers |
|---|---|---|
| CD14-positive monocyte | 0.75 | { } CD19-, CD3-, CD14+ ( ) [ CD20- ] |
| CD14-positive, CD16-low monocyte | 0.5 | { } CD19-, CD3-, CD14+ ( ) [ CD20-, C-C chemokine receptor type 2-, CD16lo ] |
| CD14-positive, CD16-positive monocyte | 0.5 | { } CD19-, CD3-, CD14+ ( ) [ CD20-, C-C chemokine receptor type 2-, CD16+ ] |
| CD14-low, CD16-positive monocyte | 0.4285714 | { } CD19-, CD3-, CD14+ ( ) [ C-C chemokine receptor type 2-, CD20-, CD16+, CX3C chemokine receptor 1hi ] |
| CD14-positive, CD16-negative classical monocyte | 0.3333333 | { } CD19-, CD3-, CD14+ ( ) [ CD20-, CD16-, high affinity immunoglobulin gamma Fc receptor I+, scavenger receptor cysteine-rich type 1 protein M130+, CX3C chemokine receptor 1lo, C-C chemokine receptor type 2hi ] |
queryNReport("CD3-CD19-CD14+CD16-CD33+CD123-CD1c-", "Monocytes")## ExpMrkrLst was not defined. Defining ExpMrkrLst as MarkerList.
##
## The phenotype of interest is CD3-CD19-CD14+CD16-CD33+CD123-CD1c-
## Marker CD14 is called CD14 molecule
## Marker CD33 is called CD33 molecule
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## Marker CD123 is called interleukin-3 receptor class 2 alpha chain
## Marker CD1c is called T-cell surface glycoprotein CD1c
## The experiment phenotype of interest is CD3,CD19,CD14,CD16,CD33,CD123,CD1c
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD14 is called CD14 molecule
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## Marker CD33 is called CD33 molecule
## Marker CD123 is called interleukin-3 receptor class 2 alpha chain
## Marker CD1c is called T-cell surface glycoprotein CD1c
## Initial query results saved in
## [current directory]/flowCL_results/results/results_CD3-CD19-CD14+CD16-CD33+CD123-CD1c-.csv
## Using a cutoff score of 3
## Parent information saved in flowCL_results/parents/parent.resCD3-CD19-CD14+CD16-CD33+CD123-CD1c-.csv## Time elapsed: 00:00:01
## Iterations at 1 out of 1
##
## Total time was: 00:00:01
## Archive saved in "[current directory]/flowCL_results/"
## [,1]
## Short marker names "CD3-CD19-CD14+CD16-CD33+CD123-CD1c-"
## Ontology marker names "CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, CD33 molecule,"
## "interleukin-3 receptor class 2 alpha chain, T-cell surface"
## "glycoprotein CD1c"
## Experiment markers "CD3,CD19,CD14,CD16,CD33,CD123,CD1c"
## Ontology exper. names "CD3 epsilon, CD19 molecule, CD14 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III, CD33 molecule,"
## "interleukin-3 receptor class 2 alpha chain, T-cell surface"
## "glycoprotein CD1c"
## Successful Match? "No"
## Marker ID "1) PR_000001892, PR_000001020, PR_000001002, PR_000001483 2)"
## "PR_000001892, PR_000001020, PR_000001002, PR_000001483 3)"
## "PR_000001889, PR_000001020, PR_000001002, PR_000001483 4)"
## "PR_000001889, PR_000001020, PR_000001002 5) PR_000001889,"
## "PR_000001020, PR_000001002 + more"
## Marker Label "1) CD33 molecule, CD3 epsilon, CD19 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III 2) CD33 molecule, CD3"
## "epsilon, CD19 molecule, low affinity immunoglobulin gamma Fc region"
## "receptor III 3) CD14 molecule, CD3 epsilon, CD19 molecule, low"
## "affinity immunoglobulin gamma Fc region receptor III 4) CD14"
## "molecule, CD3 epsilon, CD19 molecule 5) CD14 molecule, CD3 epsilon,"
## "CD19 molecule + more"
## Marker Key "1) { CD14+, CD123-, CD1c- } CD19-, CD3-, CD16-, CD33+ ( ) [ CD56-,"
## "T-cell surface glycoprotein CD8 alpha chain-, integrin alpha-M+,"
## "carcinoembryonic antigen-related cell adhesion molecule 8+, urokinase"
## "plasminogen activator surface receptor+,"
## "alpha-(1,3)-fucosyltransferase FUT4, signal transducer CD24+,"
## "aminopeptidase N+, chemokine receptor CCR1+, chemokine receptor"
## "CCR3+, CD44 molecule+, CD69 molecule+, CD9 molecule+ ] 2) { CD14+,"
## "CD123-, CD1c- } CD19-, CD3-, CD16-, CD33+ ( ) [ CD56-, T-cell surface"
## "glycoprotein CD8 alpha chain-, integrin alpha-M+, carcinoembryonic"
## "antigen-related cell adhesion molecule 8+, urokinase plasminogen"
## "activator surface receptor+, alpha-(1,3)-fucosyltransferase FUT4,"
## "signal transducer CD24+, aminopeptidase N+, low affinity"
## "immunoglobulin gamma Fc region receptor II+, leukosialin+ ] 3) {"
## "CD33+, CD123-, CD1c- } CD19-, CD3-, CD16-, CD14+ ( ) [ CD20-, high"
## "affinity immunoglobulin gamma Fc receptor I+, scavenger receptor"
## "cysteine-rich type 1 protein M130+, CX3C chemokine receptor 1lo, C-C"
## "chemokine receptor type 2hi ] 4) { CD33+, CD16-, CD123-, CD1c- }"
## "CD19-, CD3-, CD14+ ( ) [ CD34 molecule-, CD56-, CD20-, T-cell surface"
## "glycoprotein CD1a-, CD83 molecule+, integrin alpha-M+, lymphocyte"
## "antigen 75+, T-cell surface glycoprotein CD8 alpha chain+, MHC class"
## "II protein complexhi, CD86 moleculehi, CD80 moleculehi, integrin"
## "alpha-Xhi ] 5) { CD33+, CD16-, CD123-, CD1c- } CD19-, CD3-, CD14+ ( )"
## "[ CD34 molecule-, CD56-, CD20-, T-cell surface glycoprotein CD1a-,"
## "integrin alpha-M+, lymphocyte antigen 75+, T-cell surface"
## "glycoprotein CD8 alpha chain+, MHC class II protein complexlo, CD86"
## "moleculelo, CD80 moleculelo, integrin alpha-Xhi ] + more"
## Score (Out of 1) "1) -0.118 2) -0.143 3) -0.222 4) -0.333 5) -0.357 + more"
## Cell ID "1) CL_0000612 2) CL_0000580 3) CL_0002057 4) CL_0002528 5) CL_0002527"
## "+ more"
## Cell Label "1) eosinophilic myelocyte 2) neutrophilic myelocyte 3) CD14-positive,"
## "CD16-negative classical monocyte 4) mature CD14-positive dermal"
## "dendritic cell 5) immature CD14-positive dermal dendritic cell + more"
| Labels | Ranking | Markers |
|---|---|---|
| eosinophilic myelocyte | -0.1176471 | { CD14+, CD123-, CD1c- } CD19-, CD3-, CD16-, CD33+ ( ) [ CD56-, T-cell surface glycoprotein CD8 alpha chain-, integrin alpha-M+, carcinoembryonic antigen-related cell adhesion molecule 8+, urokinase plasminogen activator surface receptor+, alpha-(1,3)-fucosyltransferase FUT4, signal transducer CD24+, aminopeptidase N+, chemokine receptor CCR1+, chemokine receptor CCR3+, CD44 molecule+, CD69 molecule+, CD9 molecule+ ] |
| neutrophilic myelocyte | -0.1428571 | { CD14+, CD123-, CD1c- } CD19-, CD3-, CD16-, CD33+ ( ) [ CD56-, T-cell surface glycoprotein CD8 alpha chain-, integrin alpha-M+, carcinoembryonic antigen-related cell adhesion molecule 8+, urokinase plasminogen activator surface receptor+, alpha-(1,3)-fucosyltransferase FUT4, signal transducer CD24+, aminopeptidase N+, low affinity immunoglobulin gamma Fc region receptor II+, leukosialin+ ] |
| CD14-positive, CD16-negative classical monocyte | -0.2222222 | { CD33+, CD123-, CD1c- } CD19-, CD3-, CD16-, CD14+ ( ) [ CD20-, high affinity immunoglobulin gamma Fc receptor I+, scavenger receptor cysteine-rich type 1 protein M130+, CX3C chemokine receptor 1lo, C-C chemokine receptor type 2hi ] |
| mature CD14-positive dermal dendritic cell | -0.3333333 | { CD33+, CD16-, CD123-, CD1c- } CD19-, CD3-, CD14+ ( ) [ CD34 molecule-, CD56-, CD20-, T-cell surface glycoprotein CD1a-, CD83 molecule+, integrin alpha-M+, lymphocyte antigen 75+, T-cell surface glycoprotein CD8 alpha chain+, MHC class II protein complexhi, CD86 moleculehi, CD80 moleculehi, integrin alpha-Xhi ] |
| immature CD14-positive dermal dendritic cell | -0.3571429 | { CD33+, CD16-, CD123-, CD1c- } CD19-, CD3-, CD14+ ( ) [ CD34 molecule-, CD56-, CD20-, T-cell surface glycoprotein CD1a-, integrin alpha-M+, lymphocyte antigen 75+, T-cell surface glycoprotein CD8 alpha chain+, MHC class II protein complexlo, CD86 moleculelo, CD80 moleculelo, integrin alpha-Xhi ] |
mDC
queryNReport("CD3-CD19-CD33+CD1c+", "mDC")## ExpMrkrLst was not defined. Defining ExpMrkrLst as MarkerList.
##
## The phenotype of interest is CD3-CD19-CD33+CD1c+
## Marker CD33 is called CD33 molecule
## Marker CD1c is called T-cell surface glycoprotein CD1c
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## The experiment phenotype of interest is CD3,CD19,CD33,CD1c
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD33 is called CD33 molecule
## Marker CD1c is called T-cell surface glycoprotein CD1c
## Initial query results saved in
## [current directory]/flowCL_results/results/results_CD3-CD19-CD33+CD1c+.csv
## Using a cutoff score of 2
## Parent information saved in flowCL_results/parents/parent.resCD3-CD19-CD33+CD1c+.csv## Time elapsed: 00:00:03
## Iterations at 1 out of 1
##
## Total time was: 00:00:03
## Archive saved in "[current directory]/flowCL_results/"
## [,1]
## Short marker names "CD3-CD19-CD33+CD1c+"
## Ontology marker names "CD3 epsilon, CD19 molecule, CD33 molecule, T-cell surface"
## "glycoprotein CD1c"
## Experiment markers "CD3,CD19,CD33,CD1c"
## Ontology exper. names "CD3 epsilon, CD19 molecule, CD33 molecule, T-cell surface"
## "glycoprotein CD1c"
## Successful Match? "No"
## Marker ID "1) PR_000002027, PR_000001020, PR_000001002 2) PR_000001892,"
## "PR_000001020, PR_000001002 3) PR_000001892, PR_000001020,"
## "PR_000001002 4) PR_000001892, PR_000001020, PR_000001002 5)"
## "PR_000001892, PR_000001020, PR_000001002 + more"
## Marker Label "1) T-cell surface glycoprotein CD1c, CD3 epsilon, CD19 molecule 2)"
## "CD33 molecule, CD3 epsilon, CD19 molecule 3) CD33 molecule, CD3"
## "epsilon, CD19 molecule 4) CD33 molecule, CD3 epsilon, CD19 molecule"
## "5) CD33 molecule, CD3 epsilon, CD19 molecule + more"
## Marker Key "1) { CD33+ } CD19-, CD3-, CD1c+ ( ) [ CD34 molecule-, CD56-, CD20-,"
## "CD123-, integrin alpha-Xhi ] 2) { CD1c+ } CD19-, CD3-, CD33+ ( ) ["
## "CD56-, T-cell surface glycoprotein CD8 alpha chain-, CD16-, integrin"
## "alpha-M+, carcinoembryonic antigen-related cell adhesion molecule 8+,"
## "urokinase plasminogen activator surface receptor+,"
## "alpha-(1,3)-fucosyltransferase FUT4, signal transducer CD24+,"
## "aminopeptidase N+, low affinity immunoglobulin gamma Fc region"
## "receptor II+, leukosialin+ ] 3) { CD1c+ } CD19-, CD3-, CD33+ ( ) ["
## "CD56-, T-cell surface glycoprotein CD8 alpha chain-, fMet-Leu-Phe"
## "receptor-, integrin alpha-M+, carcinoembryonic antigen-related cell"
## "adhesion molecule 8+, urokinase plasminogen activator surface"
## "receptor+, alpha-(1,3)-fucosyltransferase FUT4, CD16+, signal"
## "transducer CD24+, aminopeptidase N+, low affinity immunoglobulin"
## "gamma Fc region receptor II+, leukosialin+ ] 4) { CD1c+ } CD19-,"
## "CD3-, CD33+ ( ) [ CD56-, T-cell surface glycoprotein CD8 alpha"
## "chain-, CD16-, integrin alpha-M+, carcinoembryonic antigen-related"
## "cell adhesion molecule 8+, urokinase plasminogen activator surface"
## "receptor+, alpha-(1,3)-fucosyltransferase FUT4, signal transducer"
## "CD24+, aminopeptidase N+, chemokine receptor CCR1+, chemokine"
## "receptor CCR3+, CD44 molecule+, CD69 molecule+, CD9 molecule+ ] 5) {"
## "CD1c+ } CD19-, CD3-, CD33+ ( ) [ CD56-, T-cell surface glycoprotein"
## "CD8 alpha chain-, CD16-, integrin alpha-M+, carcinoembryonic"
## "antigen-related cell adhesion molecule 8+, urokinase plasminogen"
## "activator surface receptor+, alpha-(1,3)-fucosyltransferase FUT4,"
## "signal transducer CD24+, aminopeptidase N+, ectonucleotide"
## "pyrophosphatase/phosphodiesterase family member 3+, tumor necrosis"
## "factor ligand superfamily member 5+, chemokine receptor CCR3hi,"
## "CD123hi, high affinity immunoglobulin epsilon receptor subunit"
## "alphahi ] + more"
## Score (Out of 1) "1) 0.125 2) 0.071 3) 0.067 4) 0.059 5) 0.059 + more"
## Cell ID "1) CL_0002399 2) CL_0000580 3) CL_0000582 4) CL_0000612 5) CL_0000614"
## "+ more"
## Cell Label "1) CD1c-positive myeloid dendritic cell 2) neutrophilic myelocyte 3)"
## "neutrophilic metamyelocyte 4) eosinophilic myelocyte 5) basophilic"
## "myelocyte + more"
| Labels | Ranking | Markers |
|---|---|---|
| CD1c-positive myeloid dendritic cell | 0.125 | { CD33+ } CD19-, CD3-, CD1c+ ( ) [ CD34 molecule-, CD56-, CD20-, CD123-, integrin alpha-Xhi ] |
| neutrophilic myelocyte | 0.07142857 | { CD1c+ } CD19-, CD3-, CD33+ ( ) [ CD56-, T-cell surface glycoprotein CD8 alpha chain-, CD16-, integrin alpha-M+, carcinoembryonic antigen-related cell adhesion molecule 8+, urokinase plasminogen activator surface receptor+, alpha-(1,3)-fucosyltransferase FUT4, signal transducer CD24+, aminopeptidase N+, low affinity immunoglobulin gamma Fc region receptor II+, leukosialin+ ] |
| neutrophilic metamyelocyte | 0.06666667 | { CD1c+ } CD19-, CD3-, CD33+ ( ) [ CD56-, T-cell surface glycoprotein CD8 alpha chain-, fMet-Leu-Phe receptor-, integrin alpha-M+, carcinoembryonic antigen-related cell adhesion molecule 8+, urokinase plasminogen activator surface receptor+, alpha-(1,3)-fucosyltransferase FUT4, CD16+, signal transducer CD24+, aminopeptidase N+, low affinity immunoglobulin gamma Fc region receptor II+, leukosialin+ ] |
| eosinophilic myelocyte | 0.05882353 | { CD1c+ } CD19-, CD3-, CD33+ ( ) [ CD56-, T-cell surface glycoprotein CD8 alpha chain-, CD16-, integrin alpha-M+, carcinoembryonic antigen-related cell adhesion molecule 8+, urokinase plasminogen activator surface receptor+, alpha-(1,3)-fucosyltransferase FUT4, signal transducer CD24+, aminopeptidase N+, chemokine receptor CCR1+, chemokine receptor CCR3+, CD44 molecule+, CD69 molecule+, CD9 molecule+ ] |
| basophilic myelocyte | 0.05882353 | { CD1c+ } CD19-, CD3-, CD33+ ( ) [ CD56-, T-cell surface glycoprotein CD8 alpha chain-, CD16-, integrin alpha-M+, carcinoembryonic antigen-related cell adhesion molecule 8+, urokinase plasminogen activator surface receptor+, alpha-(1,3)-fucosyltransferase FUT4, signal transducer CD24+, aminopeptidase N+, ectonucleotide pyrophosphatase/phosphodiesterase family member 3+, tumor necrosis factor ligand superfamily member 5+, chemokine receptor CCR3hi, CD123hi, high affinity immunoglobulin epsilon receptor subunit alphahi ] |
queryNReport("CD3-CD19-CD33+CD1c+CD16-", "mDC")## ExpMrkrLst was not defined. Defining ExpMrkrLst as MarkerList.
##
## The phenotype of interest is CD3-CD19-CD33+CD1c+CD16-
## Marker CD33 is called CD33 molecule
## Marker CD1c is called T-cell surface glycoprotein CD1c
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## The experiment phenotype of interest is CD3,CD19,CD33,CD1c,CD16
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Marker CD33 is called CD33 molecule
## Marker CD1c is called T-cell surface glycoprotein CD1c
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## Initial query results saved in
## [current directory]/flowCL_results/results/results_CD3-CD19-CD33+CD1c+CD16-.csv
## Using a cutoff score of 3
## Parent information saved in flowCL_results/parents/parent.resCD3-CD19-CD33+CD1c+CD16-.csv## Time elapsed: 00:00:01
## Iterations at 1 out of 1
##
## Total time was: 00:00:01
## Archive saved in "[current directory]/flowCL_results/"
## [,1]
## Short marker names "CD3-CD19-CD33+CD1c+CD16-"
## Ontology marker names "CD3 epsilon, CD19 molecule, CD33 molecule, T-cell surface"
## "glycoprotein CD1c, low affinity immunoglobulin gamma Fc region"
## "receptor III"
## Experiment markers "CD3,CD19,CD33,CD1c,CD16"
## Ontology exper. names "CD3 epsilon, CD19 molecule, CD33 molecule, T-cell surface"
## "glycoprotein CD1c, low affinity immunoglobulin gamma Fc region"
## "receptor III"
## Successful Match? "No"
## Marker ID "1) PR_000001892, PR_000001020, PR_000001002, PR_000001483 2)"
## "PR_000001892, PR_000001020, PR_000001002, PR_000001483 3)"
## "PR_000001892, PR_000001020, PR_000001002, PR_000001483 4)"
## "PR_000001020, PR_000001002, PR_000001483 5) PR_000002027,"
## "PR_000001020, PR_000001002 + more"
## Marker Label "1) CD33 molecule, CD3 epsilon, CD19 molecule, low affinity"
## "immunoglobulin gamma Fc region receptor III 2) CD33 molecule, CD3"
## "epsilon, CD19 molecule, low affinity immunoglobulin gamma Fc region"
## "receptor III 3) CD33 molecule, CD3 epsilon, CD19 molecule, low"
## "affinity immunoglobulin gamma Fc region receptor III 4) CD3 epsilon,"
## "CD19 molecule, low affinity immunoglobulin gamma Fc region receptor"
## "III 5) T-cell surface glycoprotein CD1c, CD3 epsilon, CD19 molecule +"
## "more"
## Marker Key "1) { CD1c+ } CD19-, CD3-, CD16-, CD33+ ( ) [ CD56-, T-cell surface"
## "glycoprotein CD8 alpha chain-, integrin alpha-M+, carcinoembryonic"
## "antigen-related cell adhesion molecule 8+, urokinase plasminogen"
## "activator surface receptor+, alpha-(1,3)-fucosyltransferase FUT4,"
## "signal transducer CD24+, aminopeptidase N+, low affinity"
## "immunoglobulin gamma Fc region receptor II+, leukosialin+ ] 2) {"
## "CD1c+ } CD19-, CD3-, CD16-, CD33+ ( ) [ CD56-, T-cell surface"
## "glycoprotein CD8 alpha chain-, integrin alpha-M+, carcinoembryonic"
## "antigen-related cell adhesion molecule 8+, urokinase plasminogen"
## "activator surface receptor+, alpha-(1,3)-fucosyltransferase FUT4,"
## "signal transducer CD24+, aminopeptidase N+, chemokine receptor CCR1+,"
## "chemokine receptor CCR3+, CD44 molecule+, CD69 molecule+, CD9"
## "molecule+ ] 3) { CD1c+ } CD19-, CD3-, CD16-, CD33+ ( ) [ CD56-,"
## "T-cell surface glycoprotein CD8 alpha chain-, integrin alpha-M+,"
## "carcinoembryonic antigen-related cell adhesion molecule 8+, urokinase"
## "plasminogen activator surface receptor+,"
## "alpha-(1,3)-fucosyltransferase FUT4, signal transducer CD24+,"
## "aminopeptidase N+, ectonucleotide pyrophosphatase/phosphodiesterase"
## "family member 3+, tumor necrosis factor ligand superfamily member 5+,"
## "chemokine receptor CCR3hi, CD123hi, high affinity immunoglobulin"
## "epsilon receptor subunit alphahi ] 4) { CD33+, CD1c+ } CD19-, CD3-,"
## "CD16- ( ) [ CD20-, CD14+, high affinity immunoglobulin gamma Fc"
## "receptor I+, scavenger receptor cysteine-rich type 1 protein M130+,"
## "CX3C chemokine receptor 1lo, C-C chemokine receptor type 2hi ] 5) {"
## "CD33+, CD16- } CD19-, CD3-, CD1c+ ( ) [ CD34 molecule-, CD56-, CD20-,"
## "CD123-, integrin alpha-Xhi ] + more"
## Score (Out of 1) "1) 0.143 2) 0.118 3) 0.118 4) -0.111 5) -0.125 + more"
## Cell ID "1) CL_0000580 2) CL_0000612 3) CL_0000614 4) CL_0002057 5) CL_0002399"
## "+ more"
## Cell Label "1) neutrophilic myelocyte 2) eosinophilic myelocyte 3) basophilic"
## "myelocyte 4) CD14-positive, CD16-negative classical monocyte 5)"
## "CD1c-positive myeloid dendritic cell + more"
| Labels | Ranking | Markers |
|---|---|---|
| neutrophilic myelocyte | 0.1428571 | { CD1c+ } CD19-, CD3-, CD16-, CD33+ ( ) [ CD56-, T-cell surface glycoprotein CD8 alpha chain-, integrin alpha-M+, carcinoembryonic antigen-related cell adhesion molecule 8+, urokinase plasminogen activator surface receptor+, alpha-(1,3)-fucosyltransferase FUT4, signal transducer CD24+, aminopeptidase N+, low affinity immunoglobulin gamma Fc region receptor II+, leukosialin+ ] |
| eosinophilic myelocyte | 0.1176471 | { CD1c+ } CD19-, CD3-, CD16-, CD33+ ( ) [ CD56-, T-cell surface glycoprotein CD8 alpha chain-, integrin alpha-M+, carcinoembryonic antigen-related cell adhesion molecule 8+, urokinase plasminogen activator surface receptor+, alpha-(1,3)-fucosyltransferase FUT4, signal transducer CD24+, aminopeptidase N+, chemokine receptor CCR1+, chemokine receptor CCR3+, CD44 molecule+, CD69 molecule+, CD9 molecule+ ] |
| basophilic myelocyte | 0.1176471 | { CD1c+ } CD19-, CD3-, CD16-, CD33+ ( ) [ CD56-, T-cell surface glycoprotein CD8 alpha chain-, integrin alpha-M+, carcinoembryonic antigen-related cell adhesion molecule 8+, urokinase plasminogen activator surface receptor+, alpha-(1,3)-fucosyltransferase FUT4, signal transducer CD24+, aminopeptidase N+, ectonucleotide pyrophosphatase/phosphodiesterase family member 3+, tumor necrosis factor ligand superfamily member 5+, chemokine receptor CCR3hi, CD123hi, high affinity immunoglobulin epsilon receptor subunit alphahi ] |
| CD14-positive, CD16-negative classical monocyte | -0.1111111 | { CD33+, CD1c+ } CD19-, CD3-, CD16- ( ) [ CD20-, CD14+, high affinity immunoglobulin gamma Fc receptor I+, scavenger receptor cysteine-rich type 1 protein M130+, CX3C chemokine receptor 1lo, C-C chemokine receptor type 2hi ] |
| CD1c-positive myeloid dendritic cell | -0.125 | { CD33+, CD16- } CD19-, CD3-, CD1c+ ( ) [ CD34 molecule-, CD56-, CD20-, CD123-, integrin alpha-Xhi ] |
queryNReport("CD56-CD16-CD14-CD33+CD123-CD1c+CD3-CD19-", "mDC")## ExpMrkrLst was not defined. Defining ExpMrkrLst as MarkerList.
##
## The phenotype of interest is CD56-CD16-CD14-CD33+CD123-CD1c+CD3-CD19-
## Marker CD33 is called CD33 molecule
## Marker CD1c is called T-cell surface glycoprotein CD1c
## Marker CD56 is called neural cell adhesion molecule 1
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## Marker CD14 is called CD14 molecule
## Marker CD123 is called interleukin-3 receptor class 2 alpha chain
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## The experiment phenotype of interest is CD56,CD16,CD14,CD33,CD123,CD1c,CD3,CD19
## Marker CD56 is called neural cell adhesion molecule 1
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## Marker CD14 is called CD14 molecule
## Marker CD33 is called CD33 molecule
## Marker CD123 is called interleukin-3 receptor class 2 alpha chain
## Marker CD1c is called T-cell surface glycoprotein CD1c
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Initial query results saved in
## [current directory]/flowCL_results/results/results_CD56-CD16-CD14-CD33+CD123-CD1c+CD3-CD19-.csv
## Using a cutoff score of 4
## Parent information saved in flowCL_results/parents/parent.resCD56-CD16-CD14-CD33+CD123-CD1c+CD3-CD19-.csv## Time elapsed: 00:00:01
## Iterations at 1 out of 1
##
## Total time was: 00:00:01
## Archive saved in "[current directory]/flowCL_results/"
## [,1]
## Short marker names "CD56-CD16-CD14-CD33+CD123-CD1c+CD3-CD19-"
## Ontology marker names "neural cell adhesion molecule 1, low affinity immunoglobulin gamma Fc"
## "region receptor III, CD14 molecule, CD33 molecule, interleukin-3"
## "receptor class 2 alpha chain, T-cell surface glycoprotein CD1c, CD3"
## "epsilon, CD19 molecule"
## Experiment markers "CD56,CD16,CD14,CD33,CD123,CD1c,CD3,CD19"
## Ontology exper. names "neural cell adhesion molecule 1, low affinity immunoglobulin gamma Fc"
## "region receptor III, CD14 molecule, CD33 molecule, interleukin-3"
## "receptor class 2 alpha chain, T-cell surface glycoprotein CD1c, CD3"
## "epsilon, CD19 molecule"
## Successful Match? "No"
## Marker ID "1) PR_000001024, PR_000001889, PR_000001865, PR_000001020,"
## "PR_000001002 2) PR_000001892, PR_000001024, PR_000001483,"
## "PR_000001020, PR_000001002 3) PR_000001892, PR_000001024,"
## "PR_000001483, PR_000001020, PR_000001002 4) PR_000002027,"
## "PR_000001024, PR_000001865, PR_000001020, PR_000001002 5)"
## "PR_000001024, PR_000001889, PR_000001020, PR_000001002 + more"
## Marker Label "1) neural cell adhesion molecule 1, CD14 molecule, interleukin-3"
## "receptor class 2 alpha chain, CD3 epsilon, CD19 molecule 2) CD33"
## "molecule, neural cell adhesion molecule 1, low affinity"
## "immunoglobulin gamma Fc region receptor III, CD3 epsilon, CD19"
## "molecule 3) CD33 molecule, neural cell adhesion molecule 1, low"
## "affinity immunoglobulin gamma Fc region receptor III, CD3 epsilon,"
## "CD19 molecule 4) T-cell surface glycoprotein CD1c, neural cell"
## "adhesion molecule 1, interleukin-3 receptor class 2 alpha chain, CD3"
## "epsilon, CD19 molecule 5) neural cell adhesion molecule 1, CD14"
## "molecule, CD3 epsilon, CD19 molecule + more"
## Marker Key "1) { CD33+, CD1c+, CD16- } CD19-, CD3-, CD56-, CD14-, CD123- ( ) ["
## "CD4-, integrin alpha-M-, CD2 molecule-, T-cell surface glycoprotein"
## "CD8 alpha chain-, CD20-, T-cell surface glycoprotein CD5-, lymphocyte"
## "antigen 6G-, Fc-gamma receptor III complex-, SLAM family member 1-,"
## "interleukin-7 receptor subunit alpha-, lymphocyte antigen 6A-2/6E-1-,"
## "integrin alpha-IIb-, transferrin receptor protein 1+, endoglin+,"
## "mast/stem cell growth factor receptor+ ] 2) { CD1c+, CD14-, CD123- }"
## "CD19-, CD3-, CD56-, CD16-, CD33+ ( ) [ T-cell surface glycoprotein"
## "CD8 alpha chain-, integrin alpha-M+, carcinoembryonic antigen-related"
## "cell adhesion molecule 8+, urokinase plasminogen activator surface"
## "receptor+, alpha-(1,3)-fucosyltransferase FUT4, signal transducer"
## "CD24+, aminopeptidase N+, chemokine receptor CCR1+, chemokine"
## "receptor CCR3+, CD44 molecule+, CD69 molecule+, CD9 molecule+ ] 3) {"
## "CD1c+, CD14-, CD123- } CD19-, CD3-, CD56-, CD16-, CD33+ ( ) [ T-cell"
## "surface glycoprotein CD8 alpha chain-, integrin alpha-M+,"
## "carcinoembryonic antigen-related cell adhesion molecule 8+, urokinase"
## "plasminogen activator surface receptor+,"
## "alpha-(1,3)-fucosyltransferase FUT4, signal transducer CD24+,"
## "aminopeptidase N+, low affinity immunoglobulin gamma Fc region"
## "receptor II+, leukosialin+ ] 4) { CD33+, CD16-, CD14- } CD19-, CD3-,"
## "CD56-, CD123-, CD1c+ ( ) [ CD34 molecule-, CD20-, integrin alpha-Xhi"
## "] 5) { CD33+, CD1c+, CD16-, CD123- } CD19-, CD3-, CD56-, CD14- ( ) ["
## "CD4-, integrin alpha-M-, CD2 molecule-, T-cell surface glycoprotein"
## "CD8 alpha chain-, CD20-, T-cell surface glycoprotein CD5-, lymphocyte"
## "antigen 6G-, lymphocyte antigen 76-, receptor-type tyrosine-protein"
## "phosphatase C isoform CD45R-, CD48 molecule-, interleukin-7 receptor"
## "subunit alpha-, natural killer cell receptor 2B4-, CD161c-, CD34"
## "molecule-, receptor-type tyrosine-protein kinase FLT3-, SLAM family"
## "member 1+, mast/stem cell growth factor receptor+, lymphocyte antigen"
## "6A-2/6E-1+, Thy-1 membrane glycoproteinlo ] + more"
## Score (Out of 1) "1) -0.05 2) -0.059 3) -0.071 4) -0.125 5) -0.174 + more"
## Cell ID "1) CL_0002000 2) CL_0000612 3) CL_0000580 4) CL_0002399 5) CL_0002034"
## "+ more"
## Cell Label "1) Kit-positive erythroid progenitor cell 2) eosinophilic myelocyte"
## "3) neutrophilic myelocyte 4) CD1c-positive myeloid dendritic cell 5)"
## "long term hematopoietic stem cell + more"
| Labels | Ranking | Markers |
|---|---|---|
| Kit-positive erythroid progenitor cell | -0.05 | { CD33+, CD1c+, CD16- } CD19-, CD3-, CD56-, CD14-, CD123- ( ) [ CD4-, integrin alpha-M-, CD2 molecule-, T-cell surface glycoprotein CD8 alpha chain-, CD20-, T-cell surface glycoprotein CD5-, lymphocyte antigen 6G-, Fc-gamma receptor III complex-, SLAM family member 1-, interleukin-7 receptor subunit alpha-, lymphocyte antigen 6A-2/6E-1-, integrin alpha-IIb-, transferrin receptor protein 1+, endoglin+, mast/stem cell growth factor receptor+ ] |
| eosinophilic myelocyte | -0.05882353 | { CD1c+, CD14-, CD123- } CD19-, CD3-, CD56-, CD16-, CD33+ ( ) [ T-cell surface glycoprotein CD8 alpha chain-, integrin alpha-M+, carcinoembryonic antigen-related cell adhesion molecule 8+, urokinase plasminogen activator surface receptor+, alpha-(1,3)-fucosyltransferase FUT4, signal transducer CD24+, aminopeptidase N+, chemokine receptor CCR1+, chemokine receptor CCR3+, CD44 molecule+, CD69 molecule+, CD9 molecule+ ] |
| neutrophilic myelocyte | -0.07142857 | { CD1c+, CD14-, CD123- } CD19-, CD3-, CD56-, CD16-, CD33+ ( ) [ T-cell surface glycoprotein CD8 alpha chain-, integrin alpha-M+, carcinoembryonic antigen-related cell adhesion molecule 8+, urokinase plasminogen activator surface receptor+, alpha-(1,3)-fucosyltransferase FUT4, signal transducer CD24+, aminopeptidase N+, low affinity immunoglobulin gamma Fc region receptor II+, leukosialin+ ] |
| CD1c-positive myeloid dendritic cell | -0.125 | { CD33+, CD16-, CD14- } CD19-, CD3-, CD56-, CD123-, CD1c+ ( ) [ CD34 molecule-, CD20-, integrin alpha-Xhi ] |
| long term hematopoietic stem cell | -0.173913 | { CD33+, CD1c+, CD16-, CD123- } CD19-, CD3-, CD56-, CD14- ( ) [ CD4-, integrin alpha-M-, CD2 molecule-, T-cell surface glycoprotein CD8 alpha chain-, CD20-, T-cell surface glycoprotein CD5-, lymphocyte antigen 6G-, lymphocyte antigen 76-, receptor-type tyrosine-protein phosphatase C isoform CD45R-, CD48 molecule-, interleukin-7 receptor subunit alpha-, natural killer cell receptor 2B4-, CD161c-, CD34 molecule-, receptor-type tyrosine-protein kinase FLT3-, SLAM family member 1+, mast/stem cell growth factor receptor+, lymphocyte antigen 6A-2/6E-1+, Thy-1 membrane glycoproteinlo ] |
queryNReport("CD56-CD16-CD14-CD123-CD1c+CD3-CD19-", "mDC")## ExpMrkrLst was not defined. Defining ExpMrkrLst as MarkerList.
##
## The phenotype of interest is CD56-CD16-CD14-CD123-CD1c+CD3-CD19-
## Marker CD1c is called T-cell surface glycoprotein CD1c
## Marker CD56 is called neural cell adhesion molecule 1
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## Marker CD14 is called CD14 molecule
## Marker CD123 is called interleukin-3 receptor class 2 alpha chain
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## The experiment phenotype of interest is CD56,CD16,CD14,CD123,CD1c,CD3,CD19
## Marker CD56 is called neural cell adhesion molecule 1
## Marker CD16 is called low affinity immunoglobulin gamma Fc region receptor III
## Marker CD14 is called CD14 molecule
## Marker CD123 is called interleukin-3 receptor class 2 alpha chain
## Marker CD1c is called T-cell surface glycoprotein CD1c
## Marker CD3 is called CD3 epsilon
## Marker CD19 is called CD19 molecule
## Initial query results saved in
## [current directory]/flowCL_results/results/results_CD56-CD16-CD14-CD123-CD1c+CD3-CD19-.csv
## Using a cutoff score of 4
## Parent information saved in flowCL_results/parents/parent.resCD56-CD16-CD14-CD123-CD1c+CD3-CD19-.csv## Time elapsed: 00:00:01
## Iterations at 1 out of 1
##
## Total time was: 00:00:01
## Archive saved in "[current directory]/flowCL_results/"
## [,1]
## Short marker names "CD56-CD16-CD14-CD123-CD1c+CD3-CD19-"
## Ontology marker names "neural cell adhesion molecule 1, low affinity immunoglobulin gamma Fc"
## "region receptor III, CD14 molecule, interleukin-3 receptor class 2"
## "alpha chain, T-cell surface glycoprotein CD1c, CD3 epsilon, CD19"
## "molecule"
## Experiment markers "CD56,CD16,CD14,CD123,CD1c,CD3,CD19"
## Ontology exper. names "neural cell adhesion molecule 1, low affinity immunoglobulin gamma Fc"
## "region receptor III, CD14 molecule, interleukin-3 receptor class 2"
## "alpha chain, T-cell surface glycoprotein CD1c, CD3 epsilon, CD19"
## "molecule"
## Successful Match? "No"
## Marker ID "1) PR_000002027, PR_000001024, PR_000001865, PR_000001020,"
## "PR_000001002 2) PR_000001024, PR_000001483, PR_000001889,"
## "PR_000001020, PR_000001002 3) PR_000001024, PR_000001889,"
## "PR_000001865, PR_000001020, PR_000001002 4) PR_000001024,"
## "PR_000001889, PR_000001020, PR_000001002 5) PR_000001024,"
## "PR_000001889, PR_000001020, PR_000001002 + more"
## Marker Label "1) T-cell surface glycoprotein CD1c, neural cell adhesion molecule 1,"
## "interleukin-3 receptor class 2 alpha chain, CD3 epsilon, CD19"
## "molecule 2) neural cell adhesion molecule 1, low affinity"
## "immunoglobulin gamma Fc region receptor III, CD14 molecule, CD3"
## "epsilon, CD19 molecule 3) neural cell adhesion molecule 1, CD14"
## "molecule, interleukin-3 receptor class 2 alpha chain, CD3 epsilon,"
## "CD19 molecule 4) neural cell adhesion molecule 1, CD14 molecule, CD3"
## "epsilon, CD19 molecule 5) neural cell adhesion molecule 1, CD14"
## "molecule, CD3 epsilon, CD19 molecule + more"
## Marker Key "1) { CD16-, CD14- } CD19-, CD3-, CD56-, CD123-, CD1c+ ( ) [ CD34"
## "molecule-, CD20-, integrin alpha-Xhi ] 2) { CD1c+, CD123- } CD19-,"
## "CD3-, CD56-, CD14-, CD16- ( ) [ CD4-, integrin alpha-M-, CD2"
## "molecule-, T-cell surface glycoprotein CD8 alpha chain-, CD20-,"
## "T-cell surface glycoprotein CD5-, lymphocyte antigen 6G-, lymphocyte"
## "antigen 76-, ADP-ribosyl cyclase 1-, CD33-, transferrin receptor"
## "protein 1-, CD34 molecule+, prominin-1+, CD59-like glycoprotein+,"
## "Thy-1 membrane glycoprotein+ ] 3) { CD1c+, CD16- } CD19-, CD3-,"
## "CD56-, CD14-, CD123- ( ) [ CD4-, integrin alpha-M-, CD2 molecule-,"
## "T-cell surface glycoprotein CD8 alpha chain-, CD20-, T-cell surface"
## "glycoprotein CD5-, lymphocyte antigen 6G-, Fc-gamma receptor III"
## "complex-, SLAM family member 1-, interleukin-7 receptor subunit"
## "alpha-, lymphocyte antigen 6A-2/6E-1-, integrin alpha-IIb-,"
## "transferrin receptor protein 1+, endoglin+, mast/stem cell growth"
## "factor receptor+ ] 4) { CD1c+, CD16-, CD123- } CD19-, CD3-, CD56-,"
## "CD14- ( ) [ CD4-, integrin alpha-M-, CD2 molecule-, T-cell surface"
## "glycoprotein CD8 alpha chain-, CD20-, T-cell surface glycoprotein"
## "CD5-, lymphocyte antigen 6G-, lymphocyte antigen 76-, receptor-type"
## "tyrosine-protein phosphatase C isoform CD45R-, CD48 molecule-,"
## "interleukin-7 receptor subunit alpha-, natural killer cell receptor"
## "2B4-, CD161c-, CD34 molecule-, receptor-type tyrosine-protein kinase"
## "FLT3-, SLAM family member 1+, mast/stem cell growth factor receptor+,"
## "lymphocyte antigen 6A-2/6E-1+, Thy-1 membrane glycoproteinlo ] 5) {"
## "CD1c+, CD16-, CD123- } CD19-, CD3-, CD56-, CD14- ( ) [ CD4-, integrin"
## "alpha-M-, CD2 molecule-, T-cell surface glycoprotein CD8 alpha"
## "chain-, CD20-, T-cell surface glycoprotein CD5-, lymphocyte antigen"
## "6G-, lymphocyte antigen 76-, receptor-type tyrosine-protein"
## "phosphatase C isoform CD45R-, CD48 molecule-, interleukin-7 receptor"
## "subunit alpha-, natural killer cell receptor 2B4-, CD161c-,"
## "receptor-type tyrosine-protein kinase FLT3-, SLAM family member 1+,"
## "mast/stem cell growth factor receptor+, lymphocyte antigen"
## "6A-2/6E-1+, CD34 molecule+ ] + more"
## Score (Out of 1) "1) 0.125 2) 0.05 3) 0.05 4) -0.087 5) -0.091 + more"
## Cell ID "1) CL_0002399 2) CL_0001024 3) CL_0002000 4) CL_0002034 5) CL_0002033"
## "+ more"
## Cell Label "1) CD1c-positive myeloid dendritic cell 2) CD34-positive,"
## "CD38-negative hematopoietic stem cell 3) Kit-positive erythroid"
## "progenitor cell 4) long term hematopoietic stem cell 5) short term"
## "hematopoietic stem cell + more"
| Labels | Ranking | Markers |
|---|---|---|
| CD1c-positive myeloid dendritic cell | 0.125 | { CD16-, CD14- } CD19-, CD3-, CD56-, CD123-, CD1c+ ( ) [ CD34 molecule-, CD20-, integrin alpha-Xhi ] |
| CD34-positive, CD38-negative hematopoietic stem cell | 0.05 | { CD1c+, CD123- } CD19-, CD3-, CD56-, CD14-, CD16- ( ) [ CD4-, integrin alpha-M-, CD2 molecule-, T-cell surface glycoprotein CD8 alpha chain-, CD20-, T-cell surface glycoprotein CD5-, lymphocyte antigen 6G-, lymphocyte antigen 76-, ADP-ribosyl cyclase 1-, CD33-, transferrin receptor protein 1-, CD34 molecule+, prominin-1+, CD59-like glycoprotein+, Thy-1 membrane glycoprotein+ ] |
| Kit-positive erythroid progenitor cell | 0.05 | { CD1c+, CD16- } CD19-, CD3-, CD56-, CD14-, CD123- ( ) [ CD4-, integrin alpha-M-, CD2 molecule-, T-cell surface glycoprotein CD8 alpha chain-, CD20-, T-cell surface glycoprotein CD5-, lymphocyte antigen 6G-, Fc-gamma receptor III complex-, SLAM family member 1-, interleukin-7 receptor subunit alpha-, lymphocyte antigen 6A-2/6E-1-, integrin alpha-IIb-, transferrin receptor protein 1+, endoglin+, mast/stem cell growth factor receptor+ ] |
| long term hematopoietic stem cell | -0.08695652 | { CD1c+, CD16-, CD123- } CD19-, CD3-, CD56-, CD14- ( ) [ CD4-, integrin alpha-M-, CD2 molecule-, T-cell surface glycoprotein CD8 alpha chain-, CD20-, T-cell surface glycoprotein CD5-, lymphocyte antigen 6G-, lymphocyte antigen 76-, receptor-type tyrosine-protein phosphatase C isoform CD45R-, CD48 molecule-, interleukin-7 receptor subunit alpha-, natural killer cell receptor 2B4-, CD161c-, CD34 molecule-, receptor-type tyrosine-protein kinase FLT3-, SLAM family member 1+, mast/stem cell growth factor receptor+, lymphocyte antigen 6A-2/6E-1+, Thy-1 membrane glycoproteinlo ] |
| short term hematopoietic stem cell | -0.09090909 | { CD1c+, CD16-, CD123- } CD19-, CD3-, CD56-, CD14- ( ) [ CD4-, integrin alpha-M-, CD2 molecule-, T-cell surface glycoprotein CD8 alpha chain-, CD20-, T-cell surface glycoprotein CD5-, lymphocyte antigen 6G-, lymphocyte antigen 76-, receptor-type tyrosine-protein phosphatase C isoform CD45R-, CD48 molecule-, interleukin-7 receptor subunit alpha-, natural killer cell receptor 2B4-, CD161c-, receptor-type tyrosine-protein kinase FLT3-, SLAM family member 1+, mast/stem cell growth factor receptor+, lymphocyte antigen 6A-2/6E-1+, CD34 molecule+ ] |
R session packages
sessionInfo()## R version 3.2.3 (2015-12-10)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 7 x64 (build 7601) Service Pack 1
##
## locale:
## [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252
## [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
## [5] LC_TIME=French_France.1252
##
## attached base packages:
## [1] grid stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] flowCL_1.8.0 SPARQL_1.16 RCurl_1.95-4.7 bitops_1.0-6
## [5] XML_3.98-1.3 Rgraphviz_2.14.0 graph_1.48.0 knitr_1.12.3
##
## loaded via a namespace (and not attached):
## [1] digest_0.6.9 stats4_3.2.3 formatR_1.2.1
## [4] magrittr_1.5 evaluate_0.8 highr_0.5.1
## [7] stringi_1.0-1 rmarkdown_0.9.2 tools_3.2.3
## [10] stringr_1.0.0 yaml_2.1.13 parallel_3.2.3
## [13] BiocGenerics_0.16.1 htmltools_0.3