Systematically identify key genes in inflammatory and non-inflammatory breast cancer

• PDGFRβ was identified as the common hub gene in both IBC and non-IBC.
• SUMO1 and COL1A1 were identified as hub genes for IBC and non-IBC, respectively.
• The commonly and significantly altered biological processes and pathways in both IBC and non-IBC were disclosed.
• The specifically and significantly altered biological processes and pathways in IBC and non-IBC were found, respectively.

Although the gene expression in breast tumor stroma, playing a critical role in determining inflammatory breast cancer (IBC) phenotype, has been proved to be significantly different between IBC and non-inflammatory breast cancer (non-IBC), more effort needs to systematically investigate the gene expression profiles between tumor epithelium and stroma and to efficiently uncover the potential molecular networks and critical genes for IBC and non-IBC. Here, we comprehensively analyzed and compared the transcriptional profiles from IBC and non-IBC patients using hierarchical clustering, protein–protein interaction (PPI) network, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database analyses, and identified PDGFRβ, SUMO1, COL1A1, FYN, CAV1, COL5A1 and MMP2 to be the key genes for breast cancer. Interestingly, PDGFRβ was found to be the hub gene in both IBC and non-IBC; SUMO1 and COL1A1 were respectively the key genes for IBC and non-IBC. These analysis results indicated that those key genes might play important role in IBC and non-IBC and provided some clues for future studies.