TABLE 4.
GO terms (molecular function, cell compartment, and biological process) most significantly enriched from the 178 proteins differentially expressed between Alport (AS1 and AS3) and control (LT). Data obtained from Cytoscape + ClueGo, only Bonferroni corrected GO terms with p ≤ 0.1) from AS1 and to LT comparison, performed with Cytoscape + ClueGo.
| ID | Term | Term p-value corrected with Bonferroni step down | GO Levels | % Associated Genes | # Genes |
|---|---|---|---|---|---|
| GO:0070268 | cornification | 0.00 | [3, 4, 7, 8, 9] | 10.34 | 12.00 |
| GO:0030261 | chromosome condensation | 0.00 | [8] | 10.00 | 7.00 |
| GO:0031936 | negative regulation of chromatin silencing | 0.00 | [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15] | 28.57 | 4.00 |
| GO:0005882 | intermediate filament | 0.00 | [6, 7] | 4.87 | 11.00 |
| GO:0097549 | chromatin organization involved in negative regulation of transcription | 0.00 | [6, 7, 8, 9, 10, 11, 12] | 6.21 | 9.00 |
| GO:0016584 | nucleosome positioning | 0.00 | [6, 7, 8, 9] | 23.53 | 4.00 |
| GO:0006323 | DNA packaging | 0.00 | [7] | 4.21 | 11.00 |
| GO:0045095 | keratin filament | 0.00 | [7, 8] | 7.00 | 7.00 |
| GO:0006997 | nucleus organization | 0.00 | [5] | 5.26 | 8.00 |
| GO:0051291 | protein heterooligomerization | 0.01 | [7] | 14.81 | 4.00 |
| GO:0045814 | negative regulation of gene expression, epigenetic | 0.01 | [5, 6, 7] | 5.65 | 7.00 |
| GO:0048525 | negative regulation of viral process | 0.01 | [2, 3, 4] | 6.45 | 6.00 |
| GO:0060968 | regulation of gene silencing | 0.02 | [3, 4, 5, 6, 7, 8] | 4.83 | 7.00 |
| GO:0031490 | chromatin DNA binding | 0.02 | [3, 5] | 5.61 | 6.00 |
| GO:0034728 | nucleosome organization | 0.02 | [5, 6, 7] | 4.06 | 8.00 |
| GO:0070653 | high-density lipoprotein particle receptor binding | 0.03 | [5] | 50.00 | 2.00 |
| GO:0010903 | negative regulation of very-low-density lipoprotein particle remodeling | 0.03 | [3, 4, 5, 6, 7, 8, 10, 11] | 50.00 | 2.00 |
| GO:0051053 | negative regulation of DNA metabolic process | 0.04 | [4, 5, 6, 7, 8] | 4.35 | 7.00 |
| GO:0000077 | DNA damage checkpoint signaling | 0.04 | [5, 6, 7, 8, 9, 10] | 4.24 | 7.00 |
| GO:0034363 | intermediate-density lipoprotein particle | 0.05 | [5, 6] | 40.00 | 2.00 |
| GO:0000792 | heterochromatin | 0.05 | [3, 7] | 6.10 | 5.00 |
| GO:0098803 | respiratory chain complex | 0.06 | [3, 4] | 5.68 | 5.00 |
| GO:0004402 | histone acetyltransferase activity | 0.07 | [8, 9, 10, 11, 12] | 4.17 | 2.00 |
| GO:0045104 | intermediate filament cytoskeleton organization | 0.07 | [3, 6] | 7.55 | 4.00 |
| GO:0005746 | mitochondrial respirasome | 0.07 | [3, 4, 6, 7, 8, 9] | 5.56 | 5.00 |
| GO:0019646 | aerobic electron transport chain | 0.08 | [4, 6, 7, 8] | 5.32 | 5.00 |
| GO:0045324 | late endosome to vacuole transport | 0.08 | [3, 4, 5] | 11.54 | 3.00 |
| GO:2001033 | negative regulation of double-strand break repair via non-homologous end joining | 0.08 |
[6, 7, 8, 9, 10, 11] | 28.57 | 2.00 |
| GO:0061436 | establishment of skin barrier | 0.10 | [5, 6, 7, 8] | 10.71 | 3.00 |
| GO:0006334 | nucleosome assembly | 0.10 | [6, 7, 8, 9] | 4.05 | 6.00 |