Stimulated vs. Non-stimulated MAIT Cells
ZLM results
## symbolid I.x I.y
## 1: FOS 1 2
## 2: IFNG 2 1
## 3: CD52 3 5
## 4: MTHFD2 4 13
## 5: GZMB 5 4
## ---
## 1487: MYCBP 1487 694
## 1488: FAM46C 1488 4696
## 1489: THUMPD3 1489 4237
## 1490: COPS8 1490 4036
## 1491: UBE2W 1491 3857We 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 2)
## Mean % Deviance| dataset | component | V1 |
|---|---|---|
| mdc | C | 1.650106 |
| mdc | D | 4.869932 |
| MAIT | C | 4.135422 |
| MAIT | D | 5.282912 |
## % Deviance 90th Percentile| dataset | component | 90% |
|---|---|---|
| mdc | C | 4.392776 |
| mdc | D | 9.364816 |
| MAIT | C | 10.816661 |
| MAIT | D | 13.380499 |
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]
## -0.3590160954
## proteasome (M226)
## -0.2933650054
## signaling in T cells\n(II) (M35.1)
## -0.2654530340
## chaperonin mediated\nprotein folding (I)\n(M204.0)
## -0.2180985181
## spliceosome (M250)
## -0.2016985235
## chaperonin mediated\nprotein folding (II)\n(M204.1)
## -0.1958057058
## respiratory electron\ntransport chain\n(mitochondrion) (M238)
## -0.1931916437
## respiratory electron\ntransport chain\n(mitochondrion) (M219)
## -0.1656004247
## respiratory electron\ntransport chain\n(mitochondrion) (M216)
## -0.1633235288
## transcription\nelongation, RNA\npolymerase II (M234)
## -0.1629657928
## translation initiation\n(M227)
## -0.1528025990
## respiratory electron\ntransport chain\n(mitochondrion) (M231)
## -0.1495440145
## purine nucleotide\nbiosynthesis (M212)
## -0.1473252342
## translation initiation\nfactor 3 complex (M245)
## -0.1470130188
## nuclear pore complex\n(M106.0)
## -0.1436849298
## cell cycle, ATP binding\n(M144)
## -0.1315680821
## mitotic cell cycle in\nstimulated CD4 T cells\n(M4.5)
## -0.1300289382
## nucleotide metabolism\n(M181)
## -0.1142870202
## enriched for\nubiquitination (M138)
## -0.1042517065
## enriched in T cells (II)\n(M223)
## -0.0992421935
## golgi membrane (II)\n(M237)
## -0.0982934396
## cell cycle, mitotic\nphase (M230)
## -0.0976745506
## intracellular transport\n(M147)
## -0.0930669413
## T cell surface signature\n(S0)
## -0.0922234313
## cell division - E2F\ntranscription network\n(M4.8)
## -0.0886058705
## cytoskeletal remodeling\n(M32.8)
## -0.0812717313
## enriched in NK cells\n(receptor activation)\n(M61.2)
## -0.0733662231
## NK cell surface\nsignature (S1)
## -0.0719236479
## leukocyte activation and\nmigration (M45)
## -0.0685381001
## enriched in antigen\npresentation (II)\n(M95.0)
## -0.0631207917
## mitosis (TF motif\nCCAATNNSNNNGCG) (M169)
## -0.0618164395
## T cell differentiation\n(Th2) (M19)
## -0.0566007808
## KLF12 targets network\n(M32.3)
## -0.0542011145
## enriched in monocytes\n(IV) (M118.0)
## -0.0480880531
## enriched in NK cells (I)\n(M7.2)
## -0.0409704177
## signaling in T cells (I)\n(M35.0)
## -0.0392371955
## small GTPase mediated\nsignal transduction\n(M215)
## -0.0311426503
## E2F1 targets (Q4)\n(M10.1)
## -0.0304191114
## cell adhesion (GO)\n(M117)
## -0.0219926386
## amino acid metabolishm\nand transport (M154.0)
## -0.0113156747
## innate antiviral\nresponse (M150)
## -0.0108190609
## cell cycle (I) (M4.1)
## -0.0001795511
## mitotic cell division\n(M6)
## 0.0002126170
## DC surface signature\n(S5)
## 0.0006536264
## PLK1 signaling events\n(M4.2)
## 0.0010094548
## blood coagulation\n(M11.1)
## 0.0046840658
## DNA repair (M76)
## 0.0047458881
## enriched in antigen\npresentation (III)\n(M95.1)
## 0.0048822238
## double positive\nthymocytes (M126)
## 0.0056611267
## leukocyte migration\n(M88.0)
## 0.0084265132
## regulation of signal\ntransduction (M3)
## 0.0091116959
## T cell differentiation\nvia ITK and PKC (M18)
## 0.0118238187
## T cell differentiation\n(M14)
## 0.0132935877
## phosphatidylinositol\nsignaling system (M101)
## 0.0135001279
## transcription regulation\nin cell development\n(M49)
## 0.0201527800
## T cell activation and\nsignaling (M5.1)
## 0.0289074861
## enriched in NK cells\n(II) (M61.0)
## 0.0331908671
## cell division in\nstimulated CD4 T cells\n(M4.6)
## 0.0345433146
## MHC-TLR7-TLR8 cluster\n(M146)
## 0.0417165480
## AP-1 transcription\nfactor network (M20)
## 0.1193520161
## chemokines and\ninflammatory molecules\nin myeloid cells (M86.0)
## 0.1330329907
## suppression of MAPK\nsignaling (M56)
## 0.1335629734
## cell cycle and growth\narrest (M31)
## 0.1588741818
## MAIT Activation [Down]
## 0.3508645057Figure 3 GSEA Results for MAIT Data Set
Figure 2 - Heatmap of Differentially Expressed Genes and Activated MAIT Module Scores
## RStudioGD
## 2## RStudioGD
## 2Figure 4 - Residual Correlations and PCA
Supplementary Figure 10 - Residual Background Correlation
## RStudioGD
## 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 14
GSEA between non-stimulated and non-responding cells
PCA plots for ngeneson effect
## [1] 5.956767 3.843590
## RStudioGD
## 2Figure 1
Flow cytometry data
## mac version of flowJo workspace recognized.## RStudioGD
## 2## RStudioGD
## 2
