Table 6.
Biological processes, KEGG pathways, and PMIDs for the EV surface unique proteins in the HIV+Aβ group for the HIV vs. HIV+Aβ comparison.
|
Gene ontology (GO) Terms for Biological Processes
10 Most Significant Results per FDR (for All GO Terms, See Supplementary Table S2A) | |||||
| Term Description | Obs | Bgr | FDR | Matching Proteins in the Network | |
| Immune effector process | 18 | 927 | 9.47 × 10−6 | ACLY,ACTR3,AICDA,ALDOA,C1S,CDC42,GSTP,IGLL1,KPNB1,KRT1,LRP1,PGM1,PPIA,PRDX6,PYGB,PYGL,RAP1B,WDR1 | |
| Leukocyte-mediated immunity | 15 | 632 | 9.47 × 10−6 | ACLY,AICDA,ALDOA,C1S,GSTP1,IGLL1,KPNB1,KRT1,PGM1,PPIA,PRDX6,PYGB,PYGL,RAP1B,WDR1 | |
| Vesicle-mediated transport | 23 | 1699 | 9.70 × 10−6 | ACLY,ACTR3,ALDOA,ANXA1,ARF3,CDC42,F13A1,FERMT3,GSTP1,IGLL1,KPNB1,KRT1,LOXL2,LRP1,PGM1,PPIA,PRDX6,PYGB,PYGL,RAP1B,SERPINE1,UBB,WDR1 | |
| Extracellular matrix organization | 11 | 296 | 9.70 × 10−6 | COMP,FBLN1,FBN1,FBN2,LOXL2,MMP2,NID2,PLOD3,SERPINE1,SULF1,SULF2 | |
| Regulated exocytosis | 15 | 691 | 1.15 × 10−5 | ACLY,ALDOA,F13A1,FERMT3,GSTP1,KPNB1,KRT1,PGM1,PPIA,PRDX6,PYGB,PYGL,RAP1B,SERPINE1,WDR1 | |
| Response to stimulus | 51 | 7824 | 1.20 × 10−5 | ACLY,ACTC1,ACTR3,AICDA,ALDOA,ANXA1,C1S,CDC42,CHIA,CLIC1,EEF1G,EXT1,F13A1,FAS,FBLN1,FBN1,FERMT3,FLNB,FSCN1,GNB2L1,GPC1,GPC6,GPRC5A,GSTP1,HMCN1,IGLL1,KPNB1,KRT1,LDHA,LOXL2,LRP1,LTBP1,MMP2,PDIA3,PGK1,PGM1,PHGDH,PLOD3,PPIA,PRDX2,PRDX6,PYGB,PYGL,RAP1B,SERPINE1,SULF1,SULF2,THBS4,UBA1,UBB,WNT5A | |
| Negative regulation of cellular response to growth factor stimulus | 8 | 137 | 1.59 × 10−5 | FBN1,FBN2,GPC1,LTBP1,SULF1,SULF2,UBB,WNT5A | |
| Immune system process | 26 | 2370 | 2.26 × 10−5 | ACLY,ACTR3,AICDA,ALDOA,ANXA1,C1S,CDC42,CHIA,FAS,FLNB,GPC1,GSTP1,IGLL1,KPNB1,KRT1,LRP1,PDIA3,PGM1,PPIA,PRDX6,PYGB,PYGL,RAP1B,UBB,WDR1,WNT5A | |
| Carbohydrate metabolic process | 12 | 457 | 2.26 × 10−5 | ALDOA,AMY1B,CHIA,EXT1,FBN1,LDHA,LDHB,PGK1,PGM1,PYGB,PYGL,RGN | |
| Immune response | 21 | 1560 | 2.26 × 10−5 | ACLY,ACTR3,AICDA,ALDOA,ANXA1,C1S,CHIA,FAS,FLNB,GSTP1,IGLL1,KPNB1,KRT1,LRP1,PGM1,PPIA,PRDX6,PYGB,PYGL,RAP1B,WNT5A | |
| KEGG Pathways | |||||
| Term Description | Obs | Bgr | FDR | Matching Proteins in the Network | |
| Glycolysis / Gluconeogenesis | 5 | 68 | 0.00077 | ALDOA,LDHA,LDHB,PGK1,PGM1 | |
| Proteoglycans in cancer | 7 | 195 | 0.00077 | CDC42,FAS,FLNB,FLNC,GPC1,MMP2,WNT5A | |
| Focal adhesion | 6 | 197 | 0.0035 | CDC42,COMP,FLNB,FLNC,RAP1B,THBS4 | |
| Pentose phosphate pathway | 3 | 30 | 0.0068 | ALDOA,PGM1,RGN | |
| Starch and sucrose metabolism | 3 | 33 | 0.0071 | PGM1,PYGB,PYGL | |
| Metabolic pathways | 13 | 1250 | 0.0095 | ACLY,ALDOA,CHIA,EXT1,LDHA,LDHB,PGK1,PGM1,PHGDH,PRDX6,PYGB,PYGL,RGN | |
| HIF-1 signaling pathway | 4 | 98 | 0.0095 | ALDOA,LDHA,PGK1,SERPINE1 | |
| Glucagon signaling pathway | 4 | 100 | 0.0095 | LDHA,LDHB,PYGB,PYGL | |
| Malaria | 3 | 47 | 0.0104 | COMP,LRP1,THBS4 | |
| Carbon metabolism | 4 | 116 | 0.011 | ALDOA,PGK1,PHGDH,RGN | |
| Fluid shear stress and atherosclerosis | 4 | 133 | 0.0164 | GPC1,GSTA5,GSTP1,MMP2 | |
| Biosynthesis of amino acids | 3 | 72 | 0.0233 | ALDOA,PGK1,PHGDH | |
| Platinum drug resistance | 3 | 70 | 0.0233 | FAS,GSTA5,GSTP1 | |
| Necroptosis | 4 | 155 | 0.0233 | FAS,PPIA,PYGB,PYGL | |
| Complement and coagulation cascades | 3 | 78 | 0.0251 | C1S,F13A1,SERPINE1 | |
| Salmonella infection | 3 | 84 | 0.0288 | CDC42,FLNB,FLNC | |
| MAPK signaling pathway | 5 | 293 | 0.0307 | CDC42,FAS,FLNB,FLNC,RAP1B | |
| AGE-RAGE signaling pathway in diabetic complications | 3 | 98 | 0.0388 | CDC42,MMP2,SERPINE1 | |
| Human papillomavirus infection | 5 | 317 | 0.0388 | CDC42,COMP,FAS,THBS4,WNT5A | |
| Propanoate metabolism | 2 | 32 | 0.0405 | LDHA,LDHB | |
| Leukocyte transendothelial migration | 3 | 112 | 0.0476 | CDC42,MMP2,RAP1B | |
| Primary immunodeficiency | 2 | 37 | 0.0481 | AICDA,IGLL1 | |
| 10 Most Significant PMID Publications per FDR | |||||
| Term ID | Term Description | Obs | Bgr | FDR | Matching Proteins in the Network |
| PMID:23823696 | (2013) Isobaric Tagging-Based Quantification for Proteomic Analysis: A Comparative Study of Spared and Affected Muscles from mdx Mice at the Early Phase of Dystrophy. | 8 | 42 | 1.26 × 10−6 | ACLY,ALDOA,ANXA1,EEF1G,LDHB,PGM1,PPIA,PRDX2 |
| PMID:29250190 | (2017) Role of exosomes in hepatocellular carcinoma cell mobility alteration. | 7 | 34 | 8.40 × 10−6 | ANXA1,CLIC1,FBLN1,LRP1,PPIA,PYGB,PYGL |
| PMID:20140087 | (2010) Comprehensive identification and modified-site mapping of S-nitrosylated targets in prostate epithelial cells. | 9 | 103 | 9.47 × 10−6 | ALDOA,ANXA1,CLIC1,FLNB,FLNC,KPNB1,PDIA3,PGK1,PLEC |
| PMID:29360750 | (2018) Proteomic Analysis of Secretomes of Oncolytic Herpes Simplex Virus-Infected Squamous Cell Carcinoma Cells. | 7 | 37 | 9.47 × 10−6 | ACLY,ANXA1,FBN1,FLNC,FSCN1,MMP2,PRDX2 |
| PMID:26779482 | (2015) The Extracellular Matrix in Bronchopulmonary Dysplasia: Target and Source. | 7 | 41 | 1.08 × 10−5 | FBLN1,FBN1,FBN2,LOXL2,LTBP1,PLOD3,SULF2 |
| PMID:24142637 | (2013) Gastric autoantigenic proteins in Helicobacter pylori infection. | 7 | 50 | 2.96 × 10−5 | ACTR3,GSTP1,LDHB,PDIA3,PRDX2,PRDX6,WDR1 |
| PMID:26184160 | (2015) A Review: Proteomics in Nasopharyngeal Carcinoma. | 8 | 83 | 2.96 × 10−5 | ANXA1,CLIC1,KRT1,MMP2,PPIA,PRDX2,PRDX6,SERPINE1 |
| PMID:26918450 | (2016) A nuclear-directed human pancreatic ribonuclease (PE5) targets the metabolic phenotype of cancer cells. | 8 | 89 | 3.71 × 10−5 | ACLY,CLIC1,GPC1,GPC6,LDHA,PGM1,PHGDH,WNT5A |
| PMID:24223867 | (2013) Lactate-modulated induction of THBS-1 activates transforming growth factor (TGF)-beta2 and migration of glioma cells in vitro. | 6 | 31 | 5.98 × 10−5 | COMP,LDHA,LDHB,MMP2,SERPINE1,THBS4 |
| PMID:20236620 | (2010) Unraveling the mechanism of elastic fiber assembly: The roles of short fibulins. | 6 | 33 | 7.46 × 10−5 | FBLN1,FBN1,FBN2,HMCN1,LOXL2,LTBP1 |