Table 3

Canonical pathways upregulated in Her2+ compared to ER + and TNBC samples
Enriched ingenuity canonical pathways pval # of genes Genes
P L
Actin Cytoskeleton Signaling 0.0002 226 20 20 0 PFN1↑, MYL6↑, CFL1↑, ARPC5L↑, CSK↑, HRAS↑, ITGA5↑, IQGAP1↑, ITGA3↑, BCAR1↑, ACTG1↑, MYL9↑, MYL12A↑, PIP5K1C↑, ARPC2↑, RHOA↑, MYH9↑, VCL↑, ACTN1↑, MSN↑
Integrin Signaling 0.0008 205 18 18 0 MAP3K11↑, RHOC↑, ARPC5L↑, ILK↑, HRAS↑, PLCG1↑, ITGA5↑, TNK2↑, ITGA3↑, BCAR1↑, ACTG1↑, NCK2↑, ARF1↑, MYL12A↑, ARPC2↑, RHOA↑, VCL↑, ACTN1↑
Regulation of Actin-based Motility by Rho 0.001 87 11 11 0 MYL9↑, MYL12A↑, PFN1↑, CFL1↑, MYL6↑, ARPC5L↑, PIP5K1C↑, RHOC↑, ARPC2↑, RHOA↑, ARHGDIA↑
Rac Signaling 0.002 117 12 12 0 RELA↑, MAP3K11↑, CFL1↑, ARPC5L↑, PIP5K1C↑, ARPC2↑, RHOA↑, ITGA5↑, HRAS↑, SH3RF1↑, ITGA3↑, IQGAP1↑
Cdc42 Signaling 0.003 142 13 13 0 MPRIP↑, MAP3K11↑, CFL1↑, MYL6↑, ARPC5L↑, ITGA5↑, TNK2↑, ITGA3↑, IQGAP1↑, HLA-F↑, MYL9↑, MYL12A↑, ARPC2↑
ILK Signaling 0.005 182 15 14 1 RELA↑, CFL1↑, MYL6↑, RHOC↑, ILK↑, ACTG1↑, MYC↓, NCK2↑, MYL9↑, TGFB1I1↑, PPP2R1A↑, FLNA↑, RHOA↑, MYH9↑, ACTN1↑
RhoA Signaling 0.006 107 11 11 0 MYL9↑, MYL12A↑, PFN1↑, CFL1↑, MYL6↑, ARPC5L↑, PIP5K1C↑, ARPC2↑, RHOA↑, ACTG1↑, MSN↑
PI3K/AKT Signaling 0.010 129 11 10 1 RELA↑, PPP2R1A↑, NFKBIA↓, YWHAH↑, TSC2↑, TYK2↑, ILK↑, ITGA5↑, HRAS↑, ITGA3↑, NFKBIB↑
Germ Cell-Sertoli Cell Junction Signaling 0.010 159 13 13 0 MAP3K11↑, RHOC↑, TUBB2A↑, ILK↑, HRAS↑, ITGA3↑, IQGAP1↑, BCAR1↑, ACTG1↑, TUBB6↑, SORBS1↑, RHOA↑, ACTN1↑
Cardiac Hypertrophy Signaling 0.010 228 16 14 1 MAP3K11↑, CALM1↑, MYL6↑, RHOC↑, PLCG1↑, HRAS↑, PPP3CC↑, EIF2B2↑, MYL9↑, GNB1↑, PLCD3↓, MYL12A↑, PLCB4↑, RHOA↑, MAPKAPK2↑, HSPB1↑
Phospholipase C Signaling 0.01 243 16 14 0 RELA↑, MYL6↑, CALM1↑, RHOC↑, PLCG1↑, ITGA5↑, PPP1R14A↑, HRAS↑, ARHGEF17↑, PPP3CC↑, ITGA3↑, MYL9↑, GNB1↑, PLCB4↑, MYL12A↑, RHOA↑
Protein Kinase A Signaling 0.01 306 19 13 3 RELA↑, YWHAH↑, MYL6↑, CALM1↑, PPP1R14A↑, PLCG1↑, PPP1R11↑, PPP3CC↑, MYL9↑, GNB1↑, PLCD3↓, MYL12A↑, PLCB4↑, NFKBIA↓, PDE7B↓, FLNA↑, RHOA↑, NFKBIB↑, PDE6D↑
FAK Signaling 0.01 98 9 9 0 CSK↑, PLCG1↑, ITGA5↑, HRAS↑, VCL↑, ITGA3↑, TNS1↑, BCAR1↑, ACTG1↑
fMLP Signaling in Neutrophils 0.01 117 10 6 0 GNB1↑, RELA↑, PLCB4↑, NFKBIA↓, CALM1↑, ARPC5L↑, ARPC2↑, HRAS↑, PPP3CC↑, NFKBIB↑
Axonal Guidance Signaling 0.04 422 21 21 0 KLC1↑, PFN1↑, GLI2↑, PLXNA3↑, MYL6↑, CFL1↑, ARPC5L↑, TUBB2A↑, HRAS↑, TGA5↑, PPP3CC↑, ITGA3↑, BCAR1↑, NCK2↑, MYL9↑, GNB1↑, PLCB4↑, MYL12A↑, TUBB6↑, ARPC2↑, RHOA↑
Neuregulin Signaling 0.04 95 8 6 2 MYC↓, PICK1↑, PLCG1↑, ITGA5↑, HBEGF↑, HRAS↑, ITGA3↑, STAT5B↓
PAK Signaling 0.05 104 8 8 0 NCK2↑, MYL9↑, MYL12A↑, CFL1↑, MYL6↑, ITGA5↑, HRAS↑, ITGA3↑
Virus Entry via Endocytic Pathways 0.05 92 8 8 0 AP2M1↑, FLNA↑, PLCG1↑, ITGA5↑, HRAS↑, ITGA3↑, ACTG1↑, DNM2↑

pval = Benjamini-Hochberg corrected p-value, P = total number of genes known to be involved in the pathway, L = number of genes from the pathway that were also in the list of significant genes. ↑ = number of genes significantly upregulated in Her2+, ↓ = number of genes significantly downregulated in Her2+. The 18 significantly enriched pathways share 66 unique genes with 61 of those upregulated in Her2+ compared to ER + and TNBC.

Tchou et al.

Tchou et al. BMC Medical Genomics 2012 5:39   doi:10.1186/1755-8794-5-39

Open Data