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
q value
Cluster 1
Signaling events mediated by stem cell
factor receptor (c-Kit)
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
Forkhead box protein A2 (FOXA2) and FOXA3
transcription factor networks
Vascular endothelial growth factor receptor 1
(VEGFR1)–specific signals
Angiopoietin (Ang) receptor Tie2-mediated signaling0.9880
Regulation of nuclear mothers against
decapentaplegic homolog 2/3 (SMAD2/3) signaling
Signaling events mediated by protein tyrosine
phosphatase 1B (PTP1B)
Osteopontin-mediated events0.9954.5
Signaling events activated by hepatocyte growth
factor receptor (c-Met)
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