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Table 2 IPA analysis enlisting top five canonical pathways and upstream regulators in TB-HIV and HIV gene sets

From: “Tuberculosis in advanced HIV infection is associated with increased expression of IFNγ and its downstream targets”

Top pathways (upregulated)

p-value

Overlap

Overlapping Genes

Role of Macrophages, Fibroblasts and Endothelial Cells in Rheumatoid Arthritis

6.01E-06

6.3% (18/287)

SOCS3,ICAM1,TLR8,CEBPD,

IRAK3,IL1R1,

CREB5,

PDGFC,

FCGR1A,

IL18R1,

IL18RAP,

IL1R2,FOS,

NFKBIA,MAPK14,TLR5,TLR1,TCF7L2

IL-10 Signaling

3.24E-05

11.8% (8/68)

IL1R2,FOS,

SOCS3,

IL4R,NFKBIA,

MAPK14,IL1R,

IL18RAP

p38 MAPK Signaling

5.71E-05

8.5% (10/117)

IL1R2, MAPK14,TIFA,DUSP1, MKNK1,

IRAK3,IL1R1,

CREB5,

IL18RAP,

HSPB1

Toll-like Receptor Signaling

3.68E-04

9.6% (7/73)

FOS,NFKBIA,MAPK1,TLR5,

TLR1,TLR8,

IRAK3

Hepatic Fibrosis / Hepatic Stellate Cell Activation

5.09E-04

6.1% (11/181)

IL1R2,IL4R,

ICAM1,HGF, FGFR1,IGF1R,

COL4A2,IL1R, IFNAR2,

PDGFC,

IL18RAP

Upstream Regulators (upregulated)

p-value of overlap

  

Immunoglobulin

1.51E-13

  

PGR

3.23E-08

  

Lipopolysaccharide

4.31E-08

  

CSF2

4.81E-07

  

IL-1

4.98E-07

  

EIF2 Signaling

3.40E-08

7.5% (13/173)

RPS7,RPS6,

RPL4,

RPLP1,

RPL23A,

RPL22L1,

RPL37,EIF4A2,

RPL23,RPS17,

RPS4,RPL13A,RPS11

Primary Immunodeficiency Signaling

6.06E-06

13.6% (6/44)

RFX5,LCK,

ZAP70,

CD8A,UNG,

IGHD

B Cell Development

1.67E-04

14.8% (4/27)

SPN,CD79B,

HLA-DMB,IGHD

Granzyme A Signaling

6.82E-04

17.6% (3/17)

PRF1,H1FX,

APEX1

Regulation of eIF4 and p70S6K Signaling

7.64E-04

4.9% (7/143)

RPS7,RPS6,

EIF4A2,

RPS17,RPS4X,

RPS11,ITGA4

Upstream Regulators (downregulated)

p-value of overlap

  

MYCN

2.72E-09

  

Alefacept

5.84E-08

  

TCR

2.59E-06

  

Lipopolysaccharide

2.89E-06

  

IL-15

9.25E-06