title: Prioritizing human cancer microRNAs based on genes' functional consistency between microRNA and cancer.
abstract: The identification of human cancer-related microRNAs (miRNAs) is important for cancer biology research. Although several identification methods have achieved remarkable success, they have overlooked the functional information associated with miRNAs. We present a computational framework that can be used to prioritize human cancer miRNAs by measuring the association between cancer and miRNAs based on the functional consistency score (FCS) of the miRNA target genes and the cancer-related genes. This approach proved successful in identifying the validated cancer miRNAs for 11 common human cancers with area under ROC curve (AUC) ranging from 71.15% to 96.36%. The FCS method had a significant advantage over miRNA differential expression analysis when identifying cancer-related miRNAs with a fine regulatory mechanism, such as miR-27a in colorectal cancer. Furthermore, a case study examining thyroid cancer showed that the FCS method can uncover novel cancer-related miRNAs such as miR-27a/b, which were showed significantly upregulated in thyroid cancer samples by qRT-PCR analysis. Our method can be used on a web-based server, CMP (cancer miRNA prioritization) and is freely accessible at http://bioinfo.hrbmu.edu.cn/CMP. This time- and cost-effective computational framework can be a valuable complement to experimental studies and can assist with future studies of miRNA involvement in the pathogenesis of cancers.
authors: College of Bioinformatics Science and Technology, Cancer Hospital Affiliated to Harbin Medical University, Harbin, 150081, China. lixia@hrbmu.edu.cn
authors: Xia
authors: X
authors: Li
authors: Qianghu
authors: Q
authors: Wang
authors: Yan
authors: Y
authors: Zheng
authors: Sali
authors: S
authors: Lv
authors: Shangwei
authors: S
authors: Ning
authors: Jie
authors: J
authors: Sun
authors: Teng
authors: T
authors: Huang
authors: Qifan
authors: Q
authors: Zheng
authors: Huan
authors: H
authors: Ren
authors: Jin
authors: J
authors: Xu
authors: Xishan
authors: X
authors: Wang
authors: Yixue
authors: Y
authors: Li
mesh_terms: D019295:Computational Biology; D015972:Gene Expression Regulation, Neoplastic; D052138:Genes, Neoplasm; D006801:Humans; D035683:MicroRNAs / Q000378:metabolism*; D009369:Neoplasms / Q000235:genetics* / Q000378:metabolism; D013964:Thyroid Neoplasms / Q000235:genetics
chemical_list: D035683:MicroRNAs