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.