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Table 1 Enrichment results

From: Loss of heterozygosity impacts MHC expression on the immune microenvironment in CDK12-mutated prostate cancer

 

ID

Description

P-adj

TCGA_MHC-I

GO:0051249

Regulation of lymphocyte activation

1.48E−19

GO:0002460

Adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains

1.48E−19

GO:0050867

Positive regulation of cell activation

2.78E−20

GO:0002449

Lymphocyte mediated immunity

1.16 E−18

GO:0006958

Complement activation, classical pathway

2.77 E−14

GO:0006959

Humoral immune response

1.08 E−09

GO:0050853

B cell receptor signaling pathway

2.20 E−08

GO:0002440

Production of molecular mediator of immune response

7.15 E−08

GO:0042742

Defense response to bacterium

1.39 E−07

GO:0006910

Phagocytosis, recognition

5.66 E−08

TCGA _MHC-II

GO:0051249

Regulation of lymphocyte activation

2.00 E−25

GO:0042110

T cell activation

5.84 E−25

GO:0050867

Positive regulation of cell activation

9.60 E−23

GO:0007159

Leukocyte cell–cell adhesion

2.50 E−20

GO:0002460

Adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains

2.80 E−20

GO:0002443

Leukocyte mediated immunity

3.53 E−19

GO:1903037

Regulation of leukocyte cell–cell adhesion

8.17 E−19

GO:0070661

Leukocyte proliferation

1.75 E−15

GO:0046651

Lymphocyte proliferation

5.77 E−14

GO:0070663

Regulation of leukocyte proliferation

1.64 E−12

mCRPC_MHC

GO:0051251

Positive regulation of lymphocyte activation

4.87 E−15

GO:0002449

Lymphocyte mediated immunity

6.43 E−15

GO:0002253

Activation of immune response

6.67 E−15

GO:0042110

T cell activation

3.27 E−11

GO:0002460

Adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains

1.76 E−09

GO:0006959

Humoral immune response

1.21 E−06

GO:0019724

B cell mediated immunity

2.55 E−06

GO:0050863

Regulation of T cell activation

9.19 E−07

GO:0007159

Leukocyte cell–cell adhesion

3.27 E−04

GO:1903037

Regulation of leukocyte cell–cell adhesion

1.75 E−03

FMRP

GO:0019221

Cytokine-mediated signaling pathway

 < 0.001

GO:0022409

Positive regulation of cell–cell adhesion

 < 0.001

GO:0002474

Antigen processing and presentation of peptide antigen via MHC class I

 < 0.001

GO:0072182

Regulation of nephron tubule epithelial cell differentiation

 < 0.001

GO:0060333

Interferon-gamma-mediated signaling pathway

 < 0.01

GO:0002479

Antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent

 < 0.01

GO:0042127

Regulation of cell population proliferation

 < 0.01

GO:0042590

Antigen processing and presentation of exogenous peptide antigen via MHC class I

 < 0.01

GO:0010719

Negative regulation of epithelial to mesenchymal transition

 < 0.01

GO:0048640

Negative regulation of developmental growth

 < 0.01

  1. Enriched GO (BP) pathways of the upregulated genes from TCGA CDK12-Mut MHC-I and MHC-II High, mCRPC group MHC High, and for our validation FMRP cohort MHC-I High group. Enrichment analyses were performed using clusterProfiler and P-adjusted value = 0.05 as the cutoff