title: Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells.
abstract: The genome-wide transcriptome profiling of cancerous and normal tissue samples can provide insights into the molecular mechanisms of cancer initiation and progression. RNA Sequencing (RNA-Seq) is a revolutionary tool that has been used extensively in cancer research. However, no existing RNA-Seq database provides all of the following features: (i) large-scale and comprehensive data archives and analyses, including coding-transcript profiling, long non-coding RNA (lncRNA) profiling and coexpression networks; (ii) phenotype-oriented data organization and searching and (iii) the visualization of expression profiles, differential expression and regulatory networks. We have constructed the first public database that meets these criteria, the Cancer RNA-Seq Nexus (CRN, http://syslab4.nchu.edu.tw/CRN). CRN has a user-friendly web interface designed to facilitate cancer research and personalized medicine. It is an open resource for intuitive data exploration, providing coding-transcript/lncRNA expression profiles to support researchers generating new hypotheses in cancer research and personalized medicine.
authors.affiliation: Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan PhD Program in Medical Biotechnology National Chung Hsing University, Taichung 402, Taiwan.
authors.forename: Jian-Rong
authors.initials: JR
authors.lastname: Li
authors.affiliation: Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan.
authors.forename: Chuan-Hu
authors.initials: CH
authors.lastname: Sun
authors.affiliation: Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Wenyuan
authors.initials: W
authors.lastname: Li
authors.affiliation: Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan.
authors.forename: Rou-Fang
authors.initials: RF
authors.lastname: Chao
authors.affiliation: Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan.
authors.forename: Chieh-Chen
authors.initials: CC
authors.lastname: Huang
authors.affiliation: Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Xianghong Jasmine
authors.initials: XJ
authors.lastname: Zhou
authors.affiliation: Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan PhD Program in Medical Biotechnology National Chung Hsing University, Taichung 402, Taiwan jimliu@nchu.edu.tw.
authors.forename: Chun-Chi
authors.initials: CC
authors.lastname: Liu
mesh_terms: D030541:Databases, Genetic; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D006801:Humans; D009369:Neoplasms / Q000235:genetics* / Q000378:metabolism; D010641:Phenotype; D062085:RNA, Long Noncoding / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism
chemical_list: D062085:RNA, Long Noncoding; D012333:RNA, Messenger