biostudies-literatureKomura DJapan Agency for Medical Research and DevelopmentTokyo Medical and Dental UniversityJapan Society for the Promotion of Science899https://www.ebi.ac.uk/biostudies/studies/S-EPMC5103609biostudies-literatureUnknown17(1)<h4>Background</h4>Cancer microenvironment plays a vital role in cancer development and progression, and cancer-stromal interactions have been recognized as important targets for cancer therapy. However, identifying relevant and druggable cancer-stromal interactions is challenging due to the lack of quantitative methods to analyze whole cancer-stromal interactome.<h4>Results</h4>We present CASTIN (CAncer-STromal INteractome analysis), a novel framework for the evaluation of cancer-stromal interactome from RNA-Seq data using cancer xenograft models. For each ligand-receptor interaction which is derived from curated protein-protein interaction database, CASTIN summarizes gene expression profiles of cancer and stroma into three evaluation indices. These indices provide quantitative evaluationBMC genomicsCASTIN: a system for comprehensive analysis of cancer-stromal interactome.PMC51036094K11215H0428716H02481Suzuki RIshikawa SKishi KSato RFukayama MIsagawa TAburatani HYamamoto SKomura DTanaka MKatoh HTatsuno KfalseCASTIN: a system for comprehensive analysis of cancer-stromal interactome.<h4>Background</h4>Cancer microenvironment plays a vital role in cancer development and progression, and cancer-stromal interactions have been recognized as important targets for cancer therapy. However, identifying relevant and druggable cancer-stromal interactions is challenging due to the lack of quantitative methods to analyze whole cancer-stromal interactome.<h4>Results</h4>We present CASTIN (CAncer-STromal INteractome analysis), a novel framework for the evaluation of cancer-stromal interactome from RNA-Seq data using cancer xenograft models. For each ligand-receptor interaction which is derived from curated protein-protein interaction database, CASTIN summarizes gene expression profiles of cancer and stroma into three evaluation indices. These indices provide quantitative evaluation2016-01-01T00:00:00Z2016 Nov2026-06-07T07:51:44.977Z2025-05-29T20:21:40.68ZS-EPMC51036092782936210.1186/s12864-016-3207-z