Table III.
Functions and pathways separately enriched for the upregulated and downregulated genes in the grade IV, vs. grade III group.
| Category | Term | P-value | Genes (n) | Gene symbol |
|---|---|---|---|---|
| Upregulated | ||||
| BP | GO:0030198~extracellular matrix organization | 9.69E-20 | 27 | IBSP, ADAMTS14, LUM, MMP9, COL3A1, POSTN, SERPINH1, TGFBI, BCL3, LOX… |
| GO:0001944~vasculature development | 1.06E-15 | 34 | CAV1, NRP1, TNFRSF12A, COL3A1, ENPEP, TYMP, ACE, HOXA3, ANG, HMOX1… | |
| GO:0043062~extracellular structure organization | 1.42E-15 | 28 | IBSP, ADAMTS14, MMP9, LUM, COL3A1, POSTN, SERPINH1, TGFBI, BCL3, LOX… | |
| CC | GO:0044421~extracellular region part | 5.11E-28 | 87 | CTHRC1, MMP9, IGFBP6, MMP7, TNFSF14, POSTN, HP, CXCL10, ISG15, SAA2… |
| GO:0031012~extracellular matrix | 3.40E-26 | 52 | CTHRC1, MMP9, MMP7, POSTN, ANG, TGFBI, LOX, SPON2, VWA1, LOXL1… | |
| GO:0005578~proteinaceous extracellular matrix | 6.96E-26 | 50 | ADAMTS18, CTHRC1, ADAMTS14, CD248, MMP9, LUM, COL3A1, MMP7, POSTN, TIMP1… | |
| MF | GO:0005201~extracellular matrix structural constituent | 3.47E-13 | 19 | COL18A1, COL4A2, COL4A1, LUM, EFEMP2, COL3A1, CHI3L1, MGP, EMILIN2, COL5A2… |
| GO:0019838~growth factor binding | 1.25E-11 | 19 | COL4A1, IL2RA, OSMR, IGFBP6, COL3A1, ESM1, COL5A1, CD36, IL1RAP, COL1A2… | |
| GO:0030247~polysaccharide binding | 7.81E-09 | 19 | FGFR1, SUSD2, C6ORF15, POSTN, CXCL6, COL5A1, PCOLCE2, TNFAIP6, BGN, ANG… | |
| Pathway | hsa04512: ECM-receptor interaction | 1.35E-10 | 17 | IBSP, COL4A2, COL4A1, COL3A1, ITGA1, ITGA3, COL5A2, COL5A1, CD36, ITGA5… |
| hsa04510: Focal adhesion | 2.82E-09 | 23 | IBSP, CAV2, CAV1, COL4A2, COL4A1, VAV3, COL3A1, MET, ITGA1, ACTN1… | |
| hsa05322: Systemic lupus erythematosus | 2.98E-05 | 12 | HIST1H2AB, HIST2H3A, HIST2H2AA4, HIST1H4L, HIST1H2BH, ACTN1, C1R, HIST2H3C, HIST2H3D… | |
| Downregulated | ||||
| BP | GO:0019226~transmission of nerve impulse | 1.02E-14 | 34 | SYT1, SYT4, GABRB3, GLRA3, GABBR2, KCNIP2, SLC1A4, NPTX1, GAD2, S1PR1… |
| GO:0007268~synaptic transmission | 2.14E-13 | 30 | SYT1, SYT4, GABRB3, GLRA3, GABBR2, KCNIP2, SLC1A4, NPTX1, GAD2, SYN1… | |
| GO:0007267~cell-cell signaling | 5.65E-12 | 40 | SYT1, EDN3, CCL3, SYT4, GABRB3, FGF17, CAMK2G, GLRA3, FGF12, GABBR2… | |
| CC | GO:0045202~synapse | 4.37E-22 | 45 | SYT1, SEPT3, CDK5R1, ENAH, SNAP91, CLSTN2, GABRB3, SYT4, GLRA3, GABRB1… |
| GO:0044456~synapse part | 1.31E-20 | 37 | SYT1, SNAP91, CLSTN2, GABRB3, SYT4, GABRB1, GLRA3, SYT9, BCAN, ATP6V1G2… | |
| GO:0043005~neuron projection | 2.66E-11 | 31 | SNCG, SYT1, CDK5R1, CCK, ADCY2, SNCB, SYT4, GABRB3, GRIN3A, GABBR2… | |
| MF | GO:0005509~calcium ion binding | 2.79E-13 | 53 | SYT1, CLSTN2, SYT4, MASP1, SYT9, GRIN3A, KCNIP2, KCNIP3, SYP, ATP2B2…… |
| GO:0022836~gated channel activity | 4.21E-12 | 29 | KCNC2, GABRB3, GABRB1, GLRA3, GRIN3A, KCNIP2, KCNK12, KCNJ3, KCNIP3, GRIN2C…… | |
| GO:0005216~ion channel activity | 3.09E-11 | 31 | KCNC2, GABRB3, GABRB1, GLRA3, GRIN3A, KCNIP2, KCNK12, KCNJ3, KCNIP3, SLC1A4…… | |
| Pathway | hsa04080: Neuroactive ligand-receptor interaction | 9.42E-07 | 19 | GABRG2, GABRA1, THRA, PRLHR, GABRB3, GLRA3, GABRB1, ADCYAP1R1, GRIN1, GRIN3A…… |
| hsa04020: Calcium signaling pathway | 2.15E-05 | 14 | ADCY2, SLC8A2, ADCY8, CAMK2G, CACNA1I, GRIN1, GRM1, ATP2B2, CD38, GRIN2C…… | |
| hsa04720: Long-term potentiation | 1.65E-03 | 7 | GRIA2, ADCY8, GRIN2C, CAMK2G, PPP1R1A, GRIN1, GRM1 |
GO, Gene Ontology; BP, biological process; CC, cellular component; MF, molecular function.