inst/doc/MAITAnalysis/MASTAnalysis.md

In RGLab/MASTdata: This is the data used for the MAST paper

title: 'MAST: A flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA-seq data. MAIT Analysis.' author: Greg Finak, Andrew McDavid, Masanao Yajima, Jingyuan Deng, Alex Shalek, Martin Prlic, Peter Linsley, Raphael Gottardo date: "2015-05-26" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{MAIT Analysis} %\VignetteEngine{knitr::rmarkdown} \usepackage[utf8]{inputenc}

Stimulated vs. Non-stimulated MAIT Cells

# library(devtools)
# install_git("http://github.fhcrc.org/gottardo-r/MASTDataPackage")
# install_git('http://github.com/RGLab/MAST')

ZLM results

We observe 1413 differentially expressed genes without the CDR effect in the model, and 291 with the CDR effect.

Analysis of deviance for ngeneson (Supplementary Figure 4)

## Mean % Deviance

|Dataset |Component | V1| |:-------|:----------|--------:| |DC |Continuous | 1.883218| |DC |Discrete | 5.238081| |MAIT |Continuous | 4.481143| |MAIT |Discrete | 5.552008|

## % Deviance 90th Percentile

|Dataset |Component | 90%| |:-------|:----------|--------:| |DC |Continuous | 5.08754| |DC |Discrete | 10.11620| |MAIT |Continuous | 11.97647| |MAIT |Discrete | 13.89787|

Visualization of most differentially expressed genes

Heatmap of MAITs based on most differentially expressed genes

Top 100 DE genes between stimulated and non-stimulated MAIT cells.

Some of the activated MAITs have transcriptional profiles more similar to unactivated MAITS.

GSEA

##                                             MAIT Activation [Up] 
##                                                     -0.387170846 
##                                                proteasome (M226) 
##                                                     -0.314344244 
##                               signaling in T cells\n(II) (M35.1) 
##                                                     -0.284029888 
##               chaperonin mediated\nprotein folding (I)\n(M204.0) 
##                                                     -0.234708751 
##                                               spliceosome (M250) 
##                                                     -0.217178180 
##              chaperonin mediated\nprotein folding (II)\n(M204.1) 
##                                                     -0.210692830 
##    respiratory electron\ntransport chain\n(mitochondrion) (M238) 
##                                                     -0.208280866 
##    respiratory electron\ntransport chain\n(mitochondrion) (M219) 
##                                                     -0.177130940 
##             transcription\nelongation, RNA\npolymerase II (M234) 
##                                                     -0.174683974 
##    respiratory electron\ntransport chain\n(mitochondrion) (M216) 
##                                                     -0.174110960 
##                                   translation initiation\n(M227) 
##                                                     -0.164768496 
##    respiratory electron\ntransport chain\n(mitochondrion) (M231) 
##                                                     -0.160812206 
##                           purine nucleotide\nbiosynthesis (M212) 
##                                                     -0.158058288 
##                                  cell cycle, ATP binding\n(M144) 
##                                                     -0.140281755 
##            mitotic cell cycle in\nstimulated CD4 T cells\n(M4.5) 
##                                                     -0.139886692 
##                              enriched for\nubiquitination (M138) 
##                                                     -0.111525790 
##                                 enriched in T cells (II)\n(M223) 
##                                                     -0.105794697 
##                                cell cycle, mitotic\nphase (M230) 
##                                                     -0.104908401 
##                   amino acid metabolishm\nand transport (M154.0) 
##                                                     -0.009385202 
##                                       DC surface signature\n(S5) 
##                                                      0.002800602 
##                                    PLK1 signaling events\n(M4.2) 
##                                                      0.003366226 
##                                     leukocyte migration\n(M88.0) 
##                                                      0.011845211 
##             transcription regulation\nin cell development\n(M49) 
##                                                      0.022981175 
##                         AP-1 transcription\nfactor network (M20) 
##                                                      0.132958000 
## chemokines and\ninflammatory molecules\nin myeloid cells (M86.0) 
##                                                      0.145395140 
##                             suppression of MAPK\nsignaling (M56) 
##                                                      0.146310102 
##                              cell cycle and growth\narrest (M31) 
##                                                      0.173068169 
##                                           MAIT Activation [Down] 
##                                                      0.381515808

Figure 4 GSEA Results for MAIT Data Set

Figure 2 - Heatmap of Differentially Expressed Genes and Activated MAIT Module Scores

## quartz_off_screen 
##                 2

## quartz_off_screen 
##                 2

Figure 3 - Residual Correlations and PCA

Supplementary Figure 3 - Residual Background Correlation

## quartz_off_screen 
##                 2

|egid |chrmap |symbol | |:------|:-------|:-------| |1831 |Xq22.3 |TSC22D3 | |5716 |Xq22.3 |PSMD10 | |122704 |14q11.2 |MRPL52 | |3002 |14q11.2 |GZMB | |51102 |1p35.3 |MECR | |93974 |1p35.3 |ATPIF1 |

Supplementary Figure 9

GSEA between non-stimulated and non-responding cells

PCA plots for ngeneson effect

RGLab/MASTdata documentation built on May 8, 2019, 5:52 a.m.