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Esophageal Carcinoma (ESCA) and Stomach Adenocarcinoma (STAD) are two types of malignant tumors in the digestive tract. Understanding common and distinct molecular mechanisms of ESCA and STAD is extremely crucial.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Results<\/jats:title>\n<jats:p>In this paper, we presented a computational framework to explore common and distinct FFLs, and molecular biomarkers for ESCA and STAD. We identified FFLs by combining regulation pairs and RNA-seq data. Then we constructed disease-specific co-expression networks based on the FFLs identified. We also used random walk with restart (RWR) on disease-specific co-expression networks to prioritize candidate molecules. We identified 148 and 242 FFLs for these two types of cancer, respectively. And we found that one TF, <jats:italic>E2F3<\/jats:italic> was related to ESCA, two genes, <jats:italic>DTNA<\/jats:italic> and <jats:italic>KCNMA1<\/jats:italic> were related to STAD, while one TF <jats:italic>ESR1<\/jats:italic> and one gene <jats:italic>KIT<\/jats:italic> were associated with both of the two types of cancer.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Conclusions<\/jats:title>\n<jats:p>This proposed computational framework predicted disease-related biomolecules effectively and discovered the correlation between two types of cancers, which helped develop the diagnostic and therapeutic strategies of Esophageal Carcinoma and Stomach Adenocarcinoma.<\/jats:p>\n<\/jats:sec>","DOI":"10.1186\/s12859-019-3230-6","type":"journal-article","created":{"date-parts":[[2019,12,30]],"date-time":"2019-12-30T08:02:27Z","timestamp":1577692947000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["The exploration of disease-specific gene regulatory networks in esophageal carcinoma and stomach adenocarcinoma"],"prefix":"10.1186","volume":"20","author":[{"given":"Guimin","family":"Qin","sequence":"first","affiliation":[]},{"given":"Luqiong","family":"Yang","sequence":"additional","affiliation":[]},{"given":"Yuying","family":"Ma","sequence":"additional","affiliation":[]},{"given":"Jiayan","family":"Liu","sequence":"additional","affiliation":[]},{"given":"Qiuyan","family":"Huo","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2019,12,30]]},"reference":[{"issue":"9864","key":"3230_CR1","doi-asserted-by":"publisher","first-page":"400","DOI":"10.1016\/S0140-6736(12)60643-6","volume":"381","author":"A Pennathur","year":"2013","unstructured":"Pennathur A, Gibson MK, Jobe BA, Luketich JD. 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