title: Clinic-genomic association mining for colorectal cancer using publicly available datasets.
abstract: In recent years, a growing number of researchers began to focus on how to establish associations between clinical and genomic data. However, up to now, there is lack of research mining clinic-genomic associations by comprehensively analysing available gene expression data for a single disease. Colorectal cancer is one of the malignant tumours. A number of genetic syndromes have been proven to be associated with colorectal cancer. This paper presents our research on mining clinic-genomic associations for colorectal cancer under biomedical big data environment. The proposed method is engineered with multiple technologies, including extracting clinical concepts using the unified medical language system (UMLS), extracting genes through the literature mining, and mining clinic-genomic associations through statistical analysis. We applied this method to datasets extracted from both gene expression omnibus (GEO) and genetic association database (GAD). A total of 23,517 clinic-genomic associations between 139 clinical concepts and 7914 genes were obtained, of which 3474 associations between 31 clinical concepts and 1689 genes were identified as highly reliable ones. Evaluation and interpretation were performed using UMLS, KEGG, and Gephi, and potential new discoveries were explored. The proposed method is effective in mining valuable knowledge from available biomedical big data and achieves a good performance in bridging clinical data with genomic data for colorectal cancer.
authors.affiliation: Department of Biomedical Engineering, Key Laboratory for Biomedical Engineering of Ministry of Education, Zhejiang University, Hangzhou 310027, China.
authors.forename: Fang
authors.initials: F
authors.lastname: Liu
authors.affiliation: Department of Biomedical Engineering, Key Laboratory for Biomedical Engineering of Ministry of Education, Zhejiang University, Hangzhou 310027, China.
authors.forename: Yaning
authors.initials: Y
authors.lastname: Feng
authors.affiliation: General Hospital of Ningxia Medical University, Yinchuan 750004, China.
authors.forename: Zhenye
authors.initials: Z
authors.lastname: Li
authors.affiliation: Department of Biomedical Engineering, Key Laboratory for Biomedical Engineering of Ministry of Education, Zhejiang University, Hangzhou 310027, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Pan
authors.affiliation: Department of Biomedical Engineering, Key Laboratory for Biomedical Engineering of Ministry of Education, Zhejiang University, Hangzhou 310027, China.
authors.forename: Yuncong
authors.initials: Y
authors.lastname: Su
authors.affiliation: Department of Biomedical Engineering, Key Laboratory for Biomedical Engineering of Ministry of Education, Zhejiang University, Hangzhou 310027, China.
authors.forename: Rui
authors.initials: R
authors.lastname: Yang
authors.affiliation: Department of Biomedical Engineering, Key Laboratory for Biomedical Engineering of Ministry of Education, Zhejiang University, Hangzhou 310027, China.
authors.forename: Liying
authors.initials: L
authors.lastname: Song
authors.affiliation: Department of Biomedical Engineering, Key Laboratory for Biomedical Engineering of Ministry of Education, Zhejiang University, Hangzhou 310027, China.
authors.forename: Huilong
authors.initials: H
authors.lastname: Duan
authors.affiliation: Department of Biomedical Engineering, Key Laboratory for Biomedical Engineering of Ministry of Education, Zhejiang University, Hangzhou 310027, China.
authors.forename: Ning
authors.identifier: 0000-0002-6573-1061
authors.initials: N
authors.lastname: Deng
mesh_terms: D015179:Colorectal Neoplasms / Q000235:genetics / Q000378:metabolism; D057225:Data Mining / Q000379:methods*; D030541:Databases, Genetic; D066264:Datasets as Topic; D015972:Gene Expression Regulation, Neoplastic; D023281:Genomics; D006801:Humans; D012984:Software