Skip to main content

Table 3 Analysis of the overlap of the cured genes with canonical pathways annotated sets in MsigDB

From: Differential gene expression analysis of ankylosing spondylitis shows deregulation of the HLA-DRB, HLA-DQB, ITM2A, and CTLA4 genes

Gene set name

Description

Genes in overlap (number, genes)

p-value

FDR q-value

BIOCARTA CTLA-4 pathway

The co-stimulatory signal during T cell activation

7: HLA-DRB1, HLA-DRB5, HLA-DRB3, HLA-DRB4, CD3E, ICOS, CTLA-4

6e−14

1.72e−10

KEGG hematopoietic cell lineage

Hematopoietic cell lineage

9: HLA-DRB1, HLA-DRB5, HLA-DRB3, HLA-DRB4, CD3E, CD2, ITGA6, IL2RA, CD59

7.78e−13

1.12e−9

REACTOME costimulation by the CD28 FAM family

Costimulation by the CD28 family

8: HLA-DRB1, HLA-DRB5, HLA-DRB3, HLA-DRB4, CD3E, ICOS, CTLA-4, HLA-DQB1

1.07e−11

1.02e−8

KEGG cell adhesion molecules (CAMs)

Cell adhesion molecules (CAMs)

9: HLA-DRB1, HLA-DRB5, HLA-DRB3, HLA-DRB4, ICOS, CTLA-4, CD2, ITGA6, HLA-DQB1

3.77e−11

2.71e−8

REACTOME PD-1 signaling

PD-1 signaling

6: HLA-DRB1, HLA-DRB5, HLA-DRB3, HLA-DRB4, CD3E, HLA-DQB1

5.82e−11

3.34e−8

BIOCARTA TCRA pathway

Lck and Fyn tyrosine kinases in initiation of TCR activation

5: HLA-DRB1, HLA-DRB5, HLA-DRB3, HLA-DRB4, CD3E

1.4e−10

6.68e−8

REACTOME generation of second messenger molecules

Generation of second messenger molecules

6: HLA-DRB1, HLA-DRB5, HLA-DRB3, HLA-DRB4, CD3E, HLA-DQB1

4.94e−10

2.02e−7

KEGG graft-versus-host disease

Graft-versus-host disease

6: HLA-DRB1, HLA-DRB5, HLA-DRB3, HLA-DRB4, KLRD1, HLA-DQB1

6.78e−10

2.43e−7

BIOCARTA Csk pathway

Activation of Csk by cAMP-dependent protein kinase inhibits signaling through the T cell receptor

5: HLA-DRB1, HLA-DRB5, HLA-DRB3, HLA-DRB4, CD3E

1.81e−9

5.24e−7

KEGG intestinal immune network for IgA production

Intestinal immune network for IgA production

6: HLA-DRB1, HLA-DRB5, HLA-DRB3, HLA-DRB4, ICOS, HLA-DQB1

1.83e−9

5.24e−7