Cadherins Associate with Distinct Stem Cell-Related Transcription Factors to Coordinate the Maintenance of Stemness in Triple-Negative Breast Cancer

Figure 2

CDH2/4/6/17-enriched genes in breast cancer. (a) Venn diagrams showing the number of the overlaps between CDH1- and CDH2-enriched genes (left panel) and the overlaps between CDH2-, CDH4-, CDH6-, and CDH17-enriched genes (right panel). The enriched genes for each individual altered cadherin were retrieved with cBioPortal enrichments module from TCGA provisional breast datasets (complete tumor group, ). CDH1 was queried with MUT HOMDEL and other CDHs were queried with default parameters. The genes were selected with (derived from Student -test) and (derived from Benjamini-Hochberg procedure). EXP, mRNA expression level; MUT, mutation; HOMDEL, homozygous deletion; PROT, protein level as determined by reverse phase protein assay (RPPA). (b) Gene Ontology (GO) analysis of CDH2/4/6/17-enriched genes with DAVID Bioinformatics Resources 6.8. Fold enrichment indicates the magnitude of enrichment compared to population background regarding a given term. DAVID, Database for Annotation, Visualization, and Integrated Discovery. (c) Clustering analysis of top 24 out of 101 CDH2/4/6/17-enriched genes. Clustering analysis was performed in GenePattern according to the instructions. Min, minimal level; Max, maximal level. (d) Alterations of top 24 from 101 CDH2/4/6/17-enriched genes in TNBC. TNBC samples () were obtained from TCGA provisional dataset as of December 15, 2016. The data were retrieved from cBioPortal with default parameters for mutations, copy number alterations, mRNA levels, and protein levels.

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