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. 2009 Aug 12;8(11):2595–2612. doi: 10.1074/mcp.M900124-MCP200

Table II. The main biological functions, networks, and diseases extracted from profile I and their associated protein IDs as assessed with Ingenuity Pathways Analysis.

Proteins shown in italics were added to the networks by the Ingenuity Pathway Knowledge Base, which was used as a reference data set. MAPK, mitogen-activated protein kinase; ERK, extracellular signal-regulated kinase; Jnk, c-Jun NH2-terminal kinase; PLC, phospholipase C; LDL, low density lipoprotein; PDGF, platelet-derived growth factor; FSH, follicle-stimulating hormone.

Top functions Associated molecules Score Focus molecules
Networks
    Lipid metabolism, small molecule biochemistry, cancer ACAT1, acetyl-CoA C-acetyltransferase, ANXA5, ANXA6, COX2, COX4I1, COX7A2, CS, CTNND1, CYCS (includes EG:54205), cytochrome c oxidase, EGFR, ERK, HADHA, HADHB, Hsp90, HSP90B1, HSPA9, HSPD1, insulin, interferon α, Jnk, LDL, MDH2, NDUFB9, NFκB, p38 MAPK, PDGF BB, PDIA3, Pkc(s), PLC, Ras, SLC25A11, UQCRC1, UQCRFS1 49 21
    Cancer, cardiovascular disease, cell morphology ACO2, ALDH6A1, ANXA3, β-estradiol, C11ORF10, C9ORF5, CDC123, CECR5, CHCHD3, CHCHD8, CPA2, DECR1, DLST, GINS3, HNF4A, HRAS, IDH2, KRT2, KRT10, LOC284230, MINA, MYC, NFKB2, OAS1H, OLFR1508, RPL31, RPL21 (includes EG:79449), RRBP1, RSPH3, SDHA, SFXN1, SIN3A, SMAD3, TERT, TIMM50 32 15
    Energy production, nucleic acid metabolism, small molecule biochemistry Adenosine-tetraphosphatase, ALDOA, AQP4, ATP5A1, ATP5B, ATP5F1, ATP5H (includes EG:10476), ATP5H (includes EG:641434), ATP5L, ATP5O, ATP5S, ATP6AP1, ATP6V0A2, ATP6V0E2, ATP6V1C1, ATP6V1C2, ATP6V1E2, ATP6V1G3, C21ORF33, CALD1, calmodulin, Ck2, CKAP4, F-actin, FSH, H+-transporting two-sector ATPase, histone h3, Mapk, MARCKS (includes EG:4082), PKM2, PPP2R2B, SEPT11, TOMM22, TRAF6, TUFM 29 14
Top functions Associated molecules p value No. of molecules
Diseases and disorders
    Genetic disorder HSPD1, AQP4, PKM2, HADHB, RPL31, UQCRFS1, EGFR, ATP5O, CALD1, SDHA, KRT2, TUFM, ALDH6A1, HSP90B1, ATP5A1, ATP5L, KRT10, CYCS (includes EG:54205), ALDOA, MARCKS (includes EG:4082), COX2, ACAT1, PDIA3, COX7A2, HADHA, UQCRC1, C14ORF2 5.68e−06–4.62e−02 27
    Neurological disease HSPD1, KRT10, CYCS (includes EG:54205), MARCKS (includes EG:4082), AQP4, PKM2, RPL31, HADHB, EGFR, COX2, ATP5O, SDHA, ACAT1, PDIA3, TUFM, ALDH6A1, HSP90B1, COX7A2, ATP5A1, HADHA, UQCRC1, ATP5L, C14ORF2 4.05e−07–4.98e−02 23
    Hematological disease PDIA3, HSP90B1, ALDOA, ANXA6, HADHA, ANXA3, ACO2, EGFR, ANXA5, CALD1 1.55e−06–4.98e−02 10
Molecular and cellular functions
    Energy production HSPD1, CYCS (includes EG:54205), MDH2, COX4I1, ACO2, UQCRFS1, ATP5O, DLST, SDHA, ATP5A1, ATP5F1, ATP5L, UQCRC1 2.53e−06–2.52e−02 13
    Small molecule biochemistry HSPD1, CYCS (includes EG:54205), MDH2, MARCKS (includes EG:4082), HADHB, ACO2, EGFR, ATP5O, ANXA5, ACAT1, PDIA3, ALDH6A1, ATP5A1, HADHA, ATP5F1, ATP5L 2.53e−06–3.93e−02 16
    Cell death DLST, HSPD1, KRT10, CYCS (includes EG:54205), HSP90B1, HADHA, DECR1, EGFR, COX2, HSPA9, ANXA5 1.03e−03–4.98e−02 11
Top functions Associated molecules p value Ratio
Canonical pathways
    Oxidative phosphorylation SDHA, COX7A2, ATP5A1, COX4I1, NDUFB9, ATP5F1, UQCRFS1, ATP5L, UQCRC1, COX2, ATP5O 1.98e−12 11:157
    Mitochondrial dysfunction SDHA, CYCS (includes EG:54205), COX7A2, ATP5A1, COX4I1, NDUFB9, UQCRFS1, UQCRC1, COX2 3.13e−09 9:170
    Citrate cycle DLST, SDHA, MDH2, IDH2, CS, ACO2 5.60e−06 6:59
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