Supplementary file 1.
Tumor biopsies DAVID analysis
Annotation Cluster
1 Enrichment Score: 1.963865863126122
Category Term
Coun
t % PValue Genes
Fold
Enrichment Benjamini FDR BIOCARTA
h_ctla4Pathway:The Co-Stimulatory Signal During T-
cell Activation 9 0.614334471 1.59E-04 ITK, CD3G, CD3D, CD80, CD3E, ICOS, CD247, LCK, CTLA4 4.998291183 0.031063645
0.19839666 8 BIOCARTA
h_stathminPathway:Stathmin and breast cancer
resistance to antimicrotubule agents 10 0.682593857 2.52E-04
CCNB1, CD3G, CD3D, CAMK4, CD3E, CAMK2G, CD247,
CD2, CAMK2B, CAMK2A 4.220779221 0.02475357
0.31498739 3 BIOCARTA
h_tcytotoxicPathway:T Cytotoxic Cell Surface
Molecules 7 0.4778157 3.62E-04 PTPRC, CD3G, CD3D, CD8A, CD3E, CD247, CD2 6.15530303 0.023756967
0.45291450 5 BIOCARTA
h_tcraPathway:Lck and Fyn tyrosine kinases in
initiation of TCR Activation 6 0.409556314 0.002006856 PTPRC, CD3G, CD3D, CD3E, CD247, LCK 5.755608028 0.095109561
2.48446319 1 BIOCARTA h_tcrmolecule:T Cell Receptor and CD3 Complex 4 0.273037543 0.003052083 CD3G, CD3D, CD3E, CD247 10.55194805 0.114549432
3.75582629 1 BIOCARTA h_thelperPathway:T Helper Cell Surface Molecules 6 0.409556314 0.003181466 PTPRC, CD3G, CD3D, CD3E, CD247, CD2 5.275974026 0.100293628
3.91213603 7 BIOCARTA
h_ctlPathway:CTL mediated immune response against
target cells 6 0.409556314 0.006880971 CD3G, CD3D, CD3E, CD247, FASLG, GZMB 4.522263451 0.15781515
8.28396003 6 BIOCARTA h_il17Pathway:IL 17 Signaling Pathway 6 0.409556314 0.009549929 CD3G, CD3D, CD8A, CD3E, CD247, CD2 4.220779221 0.191176287 11.3234738 5 BIOCARTA h_tcapoptosisPathway:HIV Induced T Cell Apoptosis 5 0.341296928 0.010103708 CD3G, CD3D, CD3E, CD247, FASLG 5.275974026 0.182975693 11.9424099
BIOCARTA
h_cskPathway:Activation of Csk by cAMP-dependent Protein Kinase Inhibits Signaling through the T Cell
Receptor 7 0.4778157 0.013177642 PTPRC, ADCY1, CD3G, CD3D, CD3E, CD247, LCK 3.357438017 0.213356562
15.3063484 4 KEGG_PATHWAY hsa04660:T cell receptor signaling pathway 15 1.023890785 0.034039699
ITK, PTPRC, CD3G, CD8A, CD3D, CD3E, CD247, CTLA4,
MAPK11, CDK4, NRAS, ICOS, LCK, GRAP2, AKT2 1.816637324 0.382077561
36.7083859 6 BIOCARTA
h_no2il12Pathway:NO2-dependent IL 12 Pathway in
NK cells 5 0.341296928 0.068126527 CD3G, CD3D, CD3E, CD247, CD2 3.103514133 0.660432902
58.6727660 4 BIOCARTA
h_il12Pathway:IL12 and Stat4 Dependent Signaling
Pathway in Th1 Development 5 0.341296928 0.128116522 IL18R1, CD3G, CD3D, CD3E, CD247 2.512368584 0.837788338
82.0393994 1 BIOCARTA h_tob1Pathway:Role of Tob in T-cell activation 4 0.273037543 0.262802674 CD3G, CD3D, CD3E, CD247 2.221462748 0.958968818 97.8038514 BIOCARTA h_tcrPathway:T Cell Receptor Signaling Pathway 6 0.409556314 0.400416383 CD3G, CD3D, CD3E, CD247, LCK, PRKCB 1.438902007 0.982951582
99.8348562 2 KEGG_PATHWAY hsa05142:Chagas disease (American trypanosomiasis) 10 0.682593857 0.490690351
ADCY1, CD3G, CD3D, CD3E, CD247, SERPINE1, FASLG,
MAPK11, CCL5, AKT2 1.164511105 0.861152994
99.9865136 2 Annotation Cluster
2 Enrichment Score: 1.9402369170468974
Category Term
Coun
t % PValue Genes
Fold
Enrichment Benjamini FDR
KEGG_PATHWAY hsa04512:ECM-receptor interaction 18 1.228668942 6.20E-04
TNXB, COL3A1, ITGA11, COL2A1, ITGA4, COL4A6, COL5A1, HMMR, COL6A5, LAMA5, COL6A3, COL1A2,
COL6A2, LAMC2, SV2B, COL1A1, COL11A2, COL11A1 2.505706654 0.082642592
0.81627200 3
KEGG_PATHWAY hsa04974:Protein digestion and absorption 17 1.160409556 0.00197404
COL3A1, ATP1B4, COL22A1, MME, SLC7A9, COL2A1, COL4A6, COL5A1, XPNPEP2, COL6A5, COL6A3, COL1A2,
COL6A2, COL12A1, COL1A1, COL11A2, COL11A1 2.339608675 0.104044998
2.57607389 9
KEGG_PATHWAY hsa04151:PI3K-Akt signaling pathway 40 2.730375427 0.025176105
FGF7, FGFR3, FGF17, COL3A1, ITGA11, FASLG, COL2A1, IL7R, COL6A5, COL6A3, COL6A2, GYS2, IL2RG, PDGFD, COL11A2, COL11A1, AKT2, IL2RB, TNXB, ITGA4, CDK4,
COL5A1, COL4A6, BRCA1, BCL2L11, PCK1, IFNAR2, NRAS, 1.404164115 0.340962321 28.5931681 2
CD19, LAMA5, CHRM1, COL1A2, PDGFRA, GNB5, MDM2, GNB4, EFNA5, EPOR, LAMC2, COL1A1
KEGG_PATHWAY hsa05146:Amoebiasis 15 1.023890785 0.051942081
IL1R2, ADCY1, IL1R1, LAMA5, COL3A1, COL1A2, COL2A1, PRKCG, LAMC2, COL1A1, COL11A2, COL11A1, COL5A1,
COL4A6, PRKCB 1.713808796 0.422589122
50.5642455 7
KEGG_PATHWAY hsa04510:Focal adhesion 23 1.56996587 0.124251362
TNXB, COL3A1, ITGA11, COL2A1, PRKCG, ITGA4, FLNB, COL4A6, COL5A1, PRKCB, COL6A5, LAMA5, COL6A3, COL1A2, COL6A2, PDGFRA, LAMC2, COL1A1, PDGFD,
COL11A2, SHC2, COL11A1, AKT2 1.352189594 0.6116091
82.6634185 3
PBMC DAVID analysis
Annotation Cluster
1 Enrichment Score: 1.5454607981735704
Category Term Count % PValue Genes Fold
Enrichment Benjamini FDR
KEGG_PATHWAY hsa05144:Malaria 13 1.345755694 5.58E-06
ICAM1, IL6, TNF, CCL2, TLR2, CXCL8, HBA2, HBA1,
SDC2, IL12A, IL1B, THBS1, HBB 5.055514727 4.74E-04 0.00727385
KEGG_PATHWAY hsa05143:African trypanosomiasis 9 0.931677019 2.28E-04
ICAM1, IL6, TNF, F2RL1, IL12A, IL1B, HBA2, HBA1,
HBB 5.196927726 0.007236461 0.296482734
KEGG_PATHWAY hsa05323:Rheumatoid arthritis 14 1.449275362 5.99E-04
ICAM1, IL6, TNF, FLT1, CCL2, TLR2, ACP5, CXCL8,
ATP6V0C, CD80, CCL20, CCL3L1, IL1B, IL1A 3.031541174 0.015156482 0.777443008
BBID 19.Cytokine_microglia 6 0.621118012 0.001829059 LOC541472, IL6, TNF, CCL2, IL12A, IL1A 5.56937799 0.120279792 1.876817345
BBID 58.(CD40L)_immnosurveillance 7 0.724637681 0.001981967 ICAM1, LOC541472, IL6, TNF, IL12A, CXCL8, IL1A 4.467105263 0.067081726 2.032267103 BIOCARTA
h_il1rPathway:Signal transduction through
IL1R 9 0.931677019 0.004500295
IRAK2, IL1R1, IL6, TNF, IL1RAP, IL1RN, NFKBIA,
IL1B, IL1A 3.234903782 0.6139179 5.543352534
BBID 56.Macrophage_regulation_of_CD4+T_cells 5 0.517598344 0.009740422 LOC541472, IL6, TNF, IL12A, IL1A 5.105263158 0.204186678 9.633738256 BBID 18.Cytokine_astocytes 6 0.621118012 0.012058723 ICAM1, LOC541472, IL6, TNF, CCL2, CXCL8 3.828947368 0.191286312 11.79936567 BBID 114.Genomic_reformatting_Brain_Ischemia 5 0.517598344 0.014261201 EGR1, LOC541472, IL6, TNF, IL1A 4.641148325 0.182164586 13.81325346
KEGG_PATHWAY hsa05133:Pertussis 10 1.035196687 0.015750689
IL6, TNF, CFL2, IL12A, CXCL8, IL1B, SERPING1, IRF3,
NLRP3, IL1A 2.540720222 0.223551169 18.68888976
BBID 22.Cytokine-chemokine_CNS 5 0.517598344 0.01993316 LOC541472, IL6, IL12A, CXCL8, IL1A 4.254385965 0.209352113 18.80974223
BBID 110.CRHandLC-NA 4 0.414078675 0.021427672 LOC541472, IL6, TNF, IL1A 5.834586466 0.194752649 20.08195187
KEGG_PATHWAY hsa05020:Prion diseases 6 0.621118012 0.030404152 EGR1, IL6, IL1B, STIP1, HSPA5, IL1A 3.36271794 0.300843229 33.12583908
BIOCARTA
h_LairPathway:Cells and Molecules involved in local acute inflammatory
response 5 0.517598344 0.047355383 ICAM1, IL6, TNF, CXCL8, IL1A 3.488621726 0.870912341 45.84894997
BBID 97.Immune_injury_MS-lesions_MS_antigen 5 0.517598344 0.055317523 LOC541472, IL6, TNF, CD80, IL12A 3.190789474 0.392213191 44.50807861 BBID 15.T-cell_polarization-chemokine_receptors 5 0.517598344 0.067447162 LOC541472, IL6, CCR5, CXCR4, IL12A 3.003095975 0.41906597 51.4548219 KEGG_PATHWAY hsa04640:Hematopoietic cell lineage 9 0.931677019 0.084104651 IL1R2, CD55, IL1R1, IL6, TNF, TFRC, FLT3, IL1B, IL1A 1.971248448 0.472746112 68.17289321 KEGG_PATHWAY hsa05332:Graft-versus-host disease 5 0.517598344 0.091484958 IL6, TNF, CD80, IL1B, IL1A 2.88718207 0.483786343 71.35767695 BIOCARTA h_cytokinePathway:Cytokine Network 5 0.517598344 0.105436717 IL6, TNF, IL12A, CXCL8, IL1A 2.695753152 0.926624954 75.55554476 KEGG_PATHWAY hsa05321:Inflammatory bowel disease (IBD) 7 0.724637681 0.116617815 IL6, TNF, TLR2, IL12A, IL1B, RORA, IL1A 2.084184557 0.555476288 80.12806857 BIOCARTA h_nfkbPathway:NF-kB Signaling Pathway 5 0.517598344 0.119744393 IL1R1, TNF, NFKBIA, TNFAIP3, IL1A 2.578546493 0.893821138 80.06367384 BIOCARTA h_granulocytesPathway:Adhesion and
Diapedesis of Granulocytes 4 0.414078675 0.124220577 ICAM1, TNF, CXCL8, IL1A 3.163017032 0.883849183 81.3082065
KEGG_PATHWAY hsa05140:Leishmaniasis 7 0.724637681 0.166101042 TNF, PTGS2, TLR2, IL12A, NFKBIA, IL1B, IL1A 1.878701572 0.634662696 90.62447245 KEGG_PATHWAY hsa04940:Type I diabetes mellitus 5 0.517598344 0.17538592 TNF, CD80, IL12A, IL1B, IL1A 2.268500198 0.641010218 91.89733278 BIOCARTA
h_inflamPathway:Cytokines and
Inflammatory Response 5 0.517598344 0.220123376 IL6, TNF, IL12A, CXCL8, IL1A 2.045054115 0.936770574 95.68681726
BBID 7.IL17_hematopoesis 3 0.310559006 0.282600452 LOC541472, IL6, CXCL8 2.784688995 0.787731707 96.78448442
BIOCARTA
h_il10Pathway:IL-10 Anti-inflammatory
Signaling Pathway 3 0.310559006 0.297805792 IL6, TNF, IL1A 2.737226277 0.966318969 98.85544372
BIOCARTA
h_lymPathway:Adhesion and Diapedesis of
Lymphocytes 3 0.310559006 0.329845867 ICAM1, CXCL8, IL1A 2.541710115 0.970366298 99.36585456
KEGG_PATHWAY
hsa04932:Non-alcoholic fatty liver disease
(NAFLD) 10 1.035196687 0.393168974
ATF4, IRS2, IL6, TNF, XBP1, ADIPOR1, CXCL8, IL1B,
PIK3R1, IL1A 1.26194713 0.821160566 99.85104182
KEGG_PATHWAY hsa05330:Allograft rejection 3 0.310559006 0.584200101 TNF, CD80, IL12A 1.545032567 0.905156966 99.99891976
Annotation Cluster
2 Enrichment Score: 1.244141910071279
Category Term Count % PValue Genes
Fold
Enrichment Benjamini FDR KEGG_PATHWAY
hsa04620:Toll-like receptor signaling
pathway 14 1.449275362 0.003390511
IL6, TNF, TLR2, CXCL8, NFKBIA, CCL4L2, CXCL10,
CD80, CCL3L1, MAP3K8, IL12A, IL1B, IRF3, PIK3R1 2.516751163 0.075712183 4.329315519 KEGG_PATHWAY
hsa05142:Chagas disease (American
trypanosomiasis) 12 1.242236025 0.019573092
GNAL, GNA15, IL6, TNF, CCL2, CCL3L1, TLR2, IL12A,
CXCL8, NFKBIA, IL1B, PIK3R1 2.198700192 0.233021404 22.70914275
KEGG_PATHWAY hsa05164:Influenza A 16 1.6563147 0.038540143
ICAM1, IL6, TNF, CCL2, NFKBIA, CXCL8, NLRP3, CXCL10, HSPA1L, CASP9, IL12A, IL1B, IRF3, DNAJC3,
IL1A, PIK3R1 1.752220842 0.341366928 40.08043279
KEGG_PATHWAY hsa05321:Inflammatory bowel disease (IBD) 7 0.724637681 0.116617815 IL6, TNF, TLR2, IL12A, IL1B, RORA, IL1A 2.084184557 0.555476288 80.12806857
KEGG_PATHWAY hsa05162:Measles 11 1.138716356 0.15788051
HSPA1L, IL6, TP53, TLR2, IL12A, NFKBIA, IL1B, IRF3,
TNFAIP3, PIK3R1, IL1A 1.576010664 0.639048545 89.34598443
KEGG_PATHWAY hsa05140:Leishmaniasis 7 0.724637681 0.166101042 TNF, PTGS2, TLR2, IL12A, NFKBIA, IL1B, IL1A 1.878701572 0.634662696 90.62447245 KEGG_PATHWAY hsa05168:Herpes simplex infection 13 1.345755694 0.249863537
IFIT1B, IL6, TNF, CCL2, TLR2, TP53, NFKBIA, PPP1CB,
DAXX, IL12A, IL1B, PER1, IRF3 1.353662413 0.74273267 97.64006484
