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

Table I. The main biological functions, networks, and diseases extracted from the rank product list and the 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; PI3K, phosphatidylinositol 3-kinase; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; Jnk, c-Jun NH2-terminal kinase; PLC, phospholipase C.

Top functions Associated molecules Score Focus molecules
Networks
    Cell-to-cell signaling and interaction, hematological disease, hematological system development and function Akt, ALB, ANXA1, ANXA2, ANXA5, ANXA6, ATP1A2, calmodulin, calpain, CALR, CANX, CD9, CKAP4, COX2, CYCS (includes EG:54205), EGFR, ERK, F-actin, GAP43, GAPDH (includes EG:2597), HSPD1, interferon α, Jnk, Mapk, MARCKS (includes EG:4082), MARCKSL1, MHC class I, NFκB, p38 MAPK, P4HB, PDIA3, PI3K, Pkc(s), PLC, Ras 47 20
    Amino acid metabolism, small molecule biochemistry, lipid metabolism Acetyl-CoA C-acetyltransferase, ASGR1, ATF4, CPT2, CS, CYC1, cytochrome bc1, FH, GANAB, GOLIM4, GOT2, HADHA, HADHB, HLA-F, HNF4A, HSPA9, IFNB1, KARS, KRT2, LETM1, MAGEA1 (includes EG:4100), MDH2, NFKB1, PELO, PYCR1, SGK1, SLC25A6, SMAD3, SSBP1, TIMM23, TIMM50, UQCRB, UQCRFS1, UQCRFSL1, UQCRH 32 15
    Energy production, nucleic acid metabolism, small molecule biochemistry Adenosine-tetraphosphatase, AGT, ATP5A1, ATP5B, ATP5C1, ATP5D, ATP5E, ATP5F1, ATP5L, ATP6V0C, β-estradiol, CR1, CRABP2, CRIP2, cyclic GMP, DECR1, FDFT1, H+-transporting two-sector ATPase, hemin, HLA-DRB1, IDH2, IFNG, MARCKSL1, MSR1, NFYA, PDIA3, PHLDA3, PKM2, PLA2G1B, RRBP1, SDHA, SLC1A3, TAP2, TOMM22 27 13
Top functions Associated molecules p value No. of molecules
Diseases and disorders
    Neurological disease ANXA2, ATP1A2, ATP5A1, ATP5L, CALR, CANX, COX2, CYCS (includes EG:54205), EGFR, GAP43, GAPDH (includes EG:2597), HADHA, HADHB, HSPD1, MARCKS (includes EG:4082), MARCKSL1, PDIA3, PKM2, SDHA, SLC1A3, SLC25A6, SSBP1, UQCRB 2.43e−07–4.87e−02 24
    Cancer ALB, ANXA1, ANXA2, PKM2, CD9, EGFR, CALR, COX2, ANXA5, ATP1A2, CANX, P4HB, GAP43, SLC25A6, CYCS (includes EG:54205), GAPDH (includes EG:2597), HSPD1, PDIA3, DECR1, SLC1A3 5.32e−06–4.98e−02 20
Molecular and cellular functions
    Energy production ATP1A2, ATP5A1, ATP5F1, ATP5L, MDH2, HSPD1, CYCS (includes EG:54205), SDHA, UQCRFS1 2.32e−06–2.64E-02 9
    Nucleic acid metabolism ATP1A2, ATP5A1, ATP5F1, ATP5L, HADHA, HSPD1, EGFR, GAPDH (includes EG:2597), CYCS (includes EG:54205) 2.32e−02–2.47e−02 9
    Small molecule biochemistry HSPD1, CALR, P4HB, MDH2, CYCS (includes EG:54205), ATP1A2, MARCKS (includes EG:4082), GANAB, HADHB, SLC1A3, EGFR, ANXA2, ANXA5, PDIA3, CD9, ATP5A1, HADHA, ATP5F1, ATP5L, ALB, PYCR1, GAPDH (includes EG:2597), CPT2, ANXA1 2.32e−06–4.53e−02 24
    Cell-to-cell signaling and interaction HSPD1, CALR, EGFR, ANXA2, ANXA5, CKAP4, KRT2, PDIA3, MARCKSL1, GAP43, CD9, ALB, ANXA1 1.24e−05–4.98e−02 13
    Molecular transport CALR, ATP1A2, MARCKS (includes EG:4082), SLC1A3, UQCRFS1, CCHCR1, SDHA, PDIA3, CD9, HADHA, ALB, ANXA1, HSPA9, CPT2, GAPDH (includes EG:2597) 2.77e−05–4.53e−02 15
Top functions Associated molecules p value Ratio
Canonical pathways
    Oxidative phosphorylation ATP5A1, ATP5F1, ATP5L, COX2, SDHA, UQCRB, UQCRFS1 5.62e−07 7:157
    Mitochondrial dysfunction ATP5A1, COX2, CYCS (includes EG:54205), SDHA, UQCRB, UQCRFS1 1.52e−05 6:170
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