Table 1.
Statistical overrepresentation in the GO biological processes of the differentially expressed proteins (DEPs) in the Apoj−/− vs WT retina as identified by the PANTHER software [94]
| DEPs/Total proteins | Fold enrichm | GO biological processes and DEPs involved |
|---|---|---|
| Oligodendrocyte differentiation (GO: 0048709) | ||
| 4/71 | 16.7 | VTN, OMG, CLU, PTPRZ1 |
| Regulation of postsynapse organization (GO: 0099175) | ||
| 4/110 | 10.8 | ABI2, PDLI5, PAK3, PPFIA2 |
| ERAD pathway (GO: 0036503) | ||
| 3/94 | 9.5 | UBE2G2, UFD1, DNJB2 |
| Glial cell differentiation (GO: 0010001) | ||
| 5/190 | 7.8 | VTN, MT3, OMG, CLU, PTPRZ1 |
| Cell–matrix adhesion (GO: 0007160) | ||
| 3/121 | 7.4 | NID1, RCC2, VTN |
| Regulation of NIK/NF-κB signaling (GO: 1901222) | ||
| 2/96 | 6.2 | AGO1, DDX3X |
| Regulation of neuron death (GO: 1901214) | ||
| 8/32 | 6.2 | RRAS2, MT3, MT1, PAK3, HRAS, CLU, CATZ, PTPRZ1 |
| Lipid homeostasis (GO: 0055088) | ||
| 3/166 | 5.4 | DDX3X, APOA1, HYES |
| Regulation of endocytosis (GO: 0030100) | ||
| 4/237 | 5.0 | SYJ2B, VTN, WDR54, CLU |
| Regulation of actin cytoskeleton organization (GO: 0032956) | ||
| 6/369 | 4.8 | ABI2, APOA1, PAK3, HRAS, BBS4 |
| Negative regulation of immune response (GO: 0050777) | ||
| 3/205 | 4.4 | THOC1, UFD1, YTHD3 |
| Regulation of vesicle-mediated transport (GO: 0060627) | ||
| 8/609 | 3.9 | APOA1, LAMP1, SYJ2B, VTN, WR54, CLU, PPFIA2, IGG2B |
| Negative regulation of gene expression (GO: 0010629) | ||
| 9/954 | 2.8 | AGO1, DDX3X, APOA1, THOC1, UFD1, YTHD3, HRAS, CATZ, BBS4 |
| Central nervous system development (GO: 0007417) | ||
| 8/877 | 2.7 | VTN, MT3, HPRT, OMG, CLU, ATRX, PTPRZ1, BBS4 |
| Regulation of MAPK cascade (GO: 0043408) | ||
| 6/722 | 2.5 | SYJ2B, MT3, WDR54, PAK3, HRAS, GAB1 |
| Regulation of response to stress (GO: 0080134) | ||
| 11/1293 | 2.5 | APOA1, TRIAP1, THOC1, LAMP1, UFD1, YTHD3, HRAS, OMG, CLU, SVIP, IGG2B |
| Regulation of cell cycle (GO: 0051726) | ||
| 8/992 | 2.4 | DDX3X, RCC2, THOC1, TIPRL, NAA10, HRAS, ATRX, BBS4 |
| Regulation of protein phosphorylation (GO: 0001932) | ||
| 9/1128 | 2.4 | DDX3X, APOA1, VTN, MT3, HRAS, CLU, PPIL4, PTPRZ1, GAB1 |
| Cell migration (GO: 0016477) | ||
| 7/899 | 2.3 | ABI2, APOA1, VTN, TM201, SCG2, BBS4, GAB1 |
| Regulation of cell death (GO: 0010941) | ||
| 13/1710 | 2.3 | DDX3X, XTRIAP1, THOC1, RRAS2, MT3, MT1, SCG2, PAK3, HMGN5, HRAS, CLU, CATZ, PTPRZ1 |
| Neurogenesis (GO: 0022008) | ||
| 10/1514 | 2.0 | ABI2, VTN, MT3, CDHR1, HPRT, PAK3, OMG, CLU, PTPRZ1, BBS4 |