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}
# library(devtools)
# install_git("http://github.fhcrc.org/gottardo-r/MASTDataPackage")
# install_git('http://github.com/RGLab/MAST')
We observe 1413 differentially expressed genes without the CDR effect in the model, and 291 with the CDR effect.
## 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|
Top 100 DE genes between stimulated and non-stimulated MAIT cells.
Some of the activated MAITs have transcriptional profiles more similar to unactivated MAITS.
## 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
## quartz_off_screen
## 2
## quartz_off_screen
## 2
## 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 |
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