Supplementary Table 2. Enrichment of GO terms and KEGG pathways of the 58 MS-associated genes.
| Category | Term | Count | % | Genes | List total | Relative enrichment | Bonferroni* |
|---|---|---|---|---|---|---|---|
| GOTERM_BP_FAT | GO:0019882~antigen processing and presentation | 12 | 21.43 | 3112, 285830, 3117, 3118, 6891, 3107, 3109, 3108, 3134, 3105, 3132, 3122 | 25 | 78.23 | 1.09×10-16 |
| GOTERM_CC_FAT | GO:0042611~MHC protein complex | 11 | 19.64 | 3112, 285830, 3117, 3118, 3107, 3109, 3108, 3134, 3105, 3132, 3122 | 24 | 102.78 | 1.06×10-16 |
| SP_PIR_KEYWORDS | mhc ii | 9 | 16.07 | 3112, 3117, 3118, 3107, 3109, 3108, 3105, 3132, 3122 | 34 | 164.25 | 1.84×10-14 |
| UP_SEQ_FEATURE | Region of interest:Connecting peptide | 9 | 16.07 | 3112, 3117, 3118, 3107, 3109, 3108, 3134, 3105, 3122 | 33 | 137.17 | 3.39×10-13 |
| UP_SEQ_FEATURE | Domain:Ig-like C1-type | 9 | 16.07 | 3112, 3117, 3118, 3107, 3109, 3108, 3134, 3105, 3122 | 33 | 130.32 | 5.42×10-13 |
| KEGG_PATHWAY | hsa05330:Allograft rejection | 9 | 16.07 | 3112, 3117, 3118, 3107, 3109, 3108, 3134, 3105, 3122 | 14 | 90.80 | 7.23×10-14 |
| KEGG_PATHWAY | hsa05332:Graft-versus-host disease | 9 | 16.07 | 3112, 3117, 3118, 3107, 3109, 3108, 3134, 3105, 3122 | 14 | 83.82 | 1.47×10-13 |
| KEGG_PATHWAY | hsa04940:Type I diabetes mellitus | 9 | 16.07 | 3112, 3117, 3118, 3107, 3109, 3108, 3134, 3105, 3122 | 14 | 77.83 | 2.80×10-13 |
| KEGG_PATHWAY | hsa04612:Antigen processing and presentation | 10 | 17.86 | 3112, 3117, 3118, 6891, 3107, 3109, 3108, 3134, 3105, 3122 | 14 | 43.76 | 7.53×10-13 |
| KEGG_PATHWAY | hsa05320:Autoimmune thyroid disease | 9 | 16.07 | 3112, 3117, 3118, 3107, 3109, 3108, 3134, 3105, 3122 | 14 | 64.10 | 1.50×10-12 |
| INTERPRO | IPR003597:Immunoglobulin C1-set | 9 | 16.07 | 3112, 3117, 3118, 3107, 3109, 3108, 3134, 3105, 3122 | 29 | 76.03 | 1.16×10-11 |
| UP_SEQ_FEATURE | Region of interest:Alpha-1 | 7 | 12.50 | 3117, 3118, 3107, 3108, 3134, 3105, 3122 | 33 | 202.71 | 1.56×10-10 |
| UP_SEQ_FEATURE | Region of interest: Alpha-2 | 7 | 12.50 | 3117, 3118, 3107, 3108, 3134, 3105, 3122 | 33 | 202.71 | 1.56×10-10 |
| INTERPRO | IPR014745:MHC class II, alpha/beta chain, N-terminal | 7 | 12.50 | 3112, 3117, 3118, 3109, 3108, 3132, 3122 | 29 | 182.78 | 7.35×10-11 |
| INTERPRO | IPR003006:Immunoglobulin/major histocompatibility complex, conserved site | 9 | 16.07 | 3112, 3117, 3118, 3107, 3109, 3108, 3134, 3105, 3122 | 29 | 59.43 | 8.98×10-11 |
| KEGG_PATHWAY | hsa05416:Viral myocarditis | 9 | 16.07 | 3112, 3117, 3118, 3107, 3109, 3108, 3134, 3105, 3122 | 14 | 46.04 | 2.47×10-11 |
| SMART | SM00407:IGc1 | 9 | 16.07 | 3112, 3117, 3118, 3107, 3109, 3108, 3134, 3105, 3122 | 24 | 50.07 | 7.27×10-11 |
| GOTERM_CC_FAT | GO:0042613~MHC class II protein complex | 7 | 12.50 | 3112, 3117, 3118, 3109, 3108, 3132, 3122 | 24 | 128.55 | 5.56×10-10 |
| GOTERM_BP_FAT | GO:0002504~antigen processing and presentation of peptide or polysaccharide antigen via MHC class II | 7 | 12.50 | 3112, 3117, 3118, 3109, 3108, 3132, 3122 | 25 | 114.78 | 3.42×10-9 |
| GOTERM_MF_FAT | GO:0032395~MHC class II receptor activity | 6 | 10.71 | 3112, 3117, 3118, 3107, 3108, 3122 | 23 | 178.26 | 7.85×10-9 |
| SP_PIR_KEYWORDS | Immune response | 10 | 17.86 | 3112, 3117, 3118, 6891, 3107, 3109, 3108, 3134, 3105, 3122 | 34 | 25.26 | 8.42×10-9 |
| KEGG_PATHWAY | hsa04514:Cell adhesion molecules (CAMs) | 9 | 16.07 | 3112, 3117, 3118, 3107, 3109, 3108, 3134, 3105, 3122 | 14 | 24.76 | 4.04×10-9 |
| GOTERM_CC_FAT | GO:0042825~TAP complex | 5 | 8.93 | 3112, 6891, 3109, 3108, 3122 | 24 | 380.42 | 2.00×10-8 |
| GOTERM_CC_FAT | GO:0042824~MHC class I peptide loading complex | 5 | 8.93 | 3112, 6891, 3109, 3108, 3122 | 24 | 295.88 | 7.18×10-8 |
| GOTERM_BP_FAT | GO:0048002~antigen processing and presentation of peptide antigen | 6 | 10.71 | 6891, 3107, 3108, 3134, 3105, 3122 | 25 | 115.95 | 2.17×10-7 |
| PIR_SUPERFAMILY | PIRSF001991:Class II histocompatibility antigen | 6 | 10.71 | 3112, 3117, 3118, 3109, 3108, 3122 | 18 | 94.82 | 2.79×10-8 |
| INTERPRO | IPR007110:Immunoglobulin-like | 11 | 19.64 | 3112, 3117, 3118, 4340, 3107, 3109, 3108, 3134, 56244, 3105, 3122 | 29 | 12.61 | 3.53×10-7 |
| KEGG_PATHWAY | hsa05310:Asthma | 6 | 10.71 | 3112, 3117, 3118, 3109, 3108, 3122 | 14 | 75.15 | 1.10×10-7 |
| GOTERM_BP_FAT | GO:0006955~immune response | 12 | 21.43 | 3112, 285830, 3117, 3118, 6891, 3107, 3109, 3108, 3134, 3105, 3132, 3122 | 25 | 9.41 | 1.53×10-6 |
| GOTERM_MF_FAT | GO:0042288~MHC class I protein binding | 5 | 8.93 | 3112, 6891, 3109, 3108, 3122 | 23 | 176.40 | 8.88×10-7 |
| INTERPRO | IPR013783:Immunoglobulin-like fold | 11 | 19.64 | 3112, 3117, 3118, 4340, 3107, 3109, 3108, 3134, 56244, 3105, 3122 | 29 | 11.43 | 9.06×10-7 |
| GOTERM_MF_FAT | GO:0042287~MHC protein binding | 5 | 8.93 | 3112, 6891, 3109, 3108, 3122 | 23 | 112.90 | 6.11×10-6 |
| KEGG_PATHWAY | hsa04672:Intestinal immune network for IgA production | 6 | 10.71 | 3112, 3117, 3118, 3109, 3108, 3122 | 14 | 44.48 | 1.72×10-6 |
| SP_PIR_KEYWORDS | Heterodimer | 6 | 10.71 | 3117, 3118, 3107, 3134, 3105, 3122 | 34 | 32.96 | 6.98×10-5 |
| SP_PIR_KEYWORDS | Transmembrane protein | 10 | 17.86 | 3112, 3117, 3118, 4340, 6891, 3107, 3108, 3134, 3105, 3122 | 34 | 8.81 | 7.59×10-5 |
| INTERPRO | IPR001003:MHC class II, alpha chain, N-terminal | 4 | 7.14 | 3117, 3118, 3108, 3122 | 29 | 191.48 | 7.32×10-5 |
| KEGG_PATHWAY | hsa05322:Systemic lupus erythematosus | 6 | 10.71 | 3112, 3117, 3118, 3109, 3108, 3122 | 14 | 22.01 | 6.04×10-5 |
| GOTERM_BP_FAT | GO:0002474~antigen processing and presentation of peptide antigen via MHC class I | 4 | 7.14 | 6891, 3107, 3134, 3105 | 25 | 127.32 | 6.60×10-4 |
| GOTERM_CC_FAT | GO:0044459~plasma membrane part | 15 | 26.79 | 4855, 3112, 3117, 3118, 6891, 394263, 285830, 199, 3107, 3109, 3108, 3134, 3105, 3132, 3122 | 24 | 3.63 | 2.43×10-4 |
| INTERPRO | IPR001039:MHC class I, alpha chain, alpha1, and alpha2 | 4 | 7.14 | 285830, 3107, 3134, 3105 | 29 | 85.10 | 9.56×10-4 |
| INTERPRO | IPR011161:MHC class I-like antigen recognition | 4 | 7.14 | 285830, 3107, 3134, 3105 | 29 | 82.06 | 1.07×10-3 |
| GOTERM_CC_FAT | GO:0042612~MHC class I protein complex | 4 | 7.14 | 285830, 3107, 3134, 3105 | 24 | 76.08 | 1.17×10-3 |
| BIOCARTA | h_mhcPathway:Antigen processing and presentation | 3 | 5.36 | 6891, 3105, 3122 | 3 | 143.70 | 5.67×10-4 |
| UP_SEQ_FEATURE | Sequence variant | 31 | 55.36 | 170679, 3112, 4855, 11074, 54535, 6891, 56244, 7148, 10919, 6941, 199, 6046, 83463, 5460, 3107, 3109, 3108, 3134, 3105, 401250, 3117, 3118, 4340, 29113, 8449, 10665, 7916, 394263, 25833, 3122, 7917 | 33 | 1.50 | 1.94×10-2 |
| SP_PIR_KEYWORDS | Polymorphism | 31 | 55.36 | 170679, 3112, 4855, 11074, 54535, 6891, 56244, 7148, 10919, 6941, 199, 6046, 83463, 5460, 3107, 3109, 3108, 3134, 3105, 401250, 3117, 3118, 4340, 29113, 8449, 10665, 7916, 394263, 25833, 3122, 7917 | 34 | 1.52 | 7.47×10-3 |
| UP_SEQ_FEATURE | Region of interest:Alpha-3 | 3 | 5.36 | 3107, 3134, 3105 | 33 | 193.06 | 2.92×10-2 |
| SP_PIR_KEYWORDS | mhc i | 3 | 5.36 | 3107, 3134, 3105 | 34 | 169.72 | 1.05×10-2 |
| GOTERM_BP_FAT | GO:0002478~antigen processing and presentation of exogenous peptide antigen | 3 | 5.36 | 6891, 3108, 3122 | 25 | 147.58 | 3.25×10-2 |
| PIR_SUPERFAMILY | PIRSF001990:Class I histocompatibility antigen | 3 | 5.36 | 3107, 3134, 3105 | 18 | 136.96 | 2.30×10-3 |
| GOTERM_BP_FAT | GO:0019884~antigen processing and presentation of exogenous antigen | 3 | 5.36 | 6891, 3108, 3122 | 25 | 115.95 | 5.30×10-2 |
| GOTERM_MF_FAT | GO:0042277~peptide binding | 5 | 8.93 | 3112, 6891, 3109, 3108, 3122 | 23 | 13.90 | 2.69×10-2 |
| INTERPRO | IPR000353:MHC class II, beta chain, N-terminal | 3 | 5.36 | 3112, 3109, 3132 | 29 | 101.37 | 2.84×10-2 |
| GOTERM_MF_FAT | GO:0032393~MHC class I receptor activity | 3 | 5.36 | 3107, 3134, 3105 | 23 | 99.61 | 2.89×10-2 |
| GOTERM_CC_FAT | GO:0005886~plasma membrane | 16 | 28.57 | 4855, 3112, 3117, 3118, 4340, 6891, 394263, 285830, 199, 3107, 3109, 3108, 3134, 3105, 3132, 3122 | 24 | 2.26 | 2.98×10-2 |
Count, the number of genes enriched in particular GO terms or KEGG pathways; Genes, potential genes enriched in particular GO terms or KEGG pathways.
*p value with Bonferroni correction for multiple tests. Only significant results with p<0.05 are listed.
GO: Gene Ontology, KEGG: Kyoto Encyclopedia of Genes and Genomes, MHC: major histocompatibility complex, MS: mltiple sclerosis.