Table 3. Selected pathways associated with each image-based cluster.

From the complete set of pathways significantly associated with each image-based cluster (table S6) are selected pathways that are either specifically differentially expressed among the three clusters or among the top 10 for the cluster by fold change.

Signaling pathwayFold
change
q value
(%)
Cluster 1
Signaling events mediated by stem cell
factor receptor (c-Kit)
1.0330
Cluster 2
Signaling events mediated by c-Kit0.9760
Signaling events mediated by prolactin (PRL)0.9974.5
Platelet-derived growth factor receptor–α
(PDGFR-α) signaling pathway
0.9970
Forkhead box protein A2 (FOXA2) and FOXA3
transcription factor networks
0.9910
Vascular endothelial growth factor receptor 1
(VEGFR1)–specific signals
0.9964.5
Angiopoietin (Ang) receptor Tie2-mediated signaling0.9880
Regulation of nuclear mothers against
decapentaplegic homolog 2/3 (SMAD2/3) signaling
0.9954.5
Signaling events mediated by protein tyrosine
phosphatase 1B (PTP1B)
0.9954.5
Osteopontin-mediated events0.9954.5
Signaling events activated by hepatocyte growth
factor receptor (c-Met)
0.9944.5
Cluster 3
FOXA2 and FOXA3 transcription factor networks1.0130
PDGFR-β signaling pathway1.0130
Canonical Wnt signaling pathway1.0033.6197
VEGFR1-specific signals1.0040
Ang receptor Tie2-mediated signaling1.0093.6197
Syndecan-1–mediated signaling events1.0110
Interleukin-6 (IL-6)–mediated signaling events1.0103.6197
Osteopontin-mediated events1.0100
Fc-ε receptor I signaling in mast cells1.0090
αMβ2 integrin signaling1.0090