title: Identification of miRNA-mRNA Modules in Colorectal Cancer Using Rough Hypercuboid Based Supervised Clustering.
abstract: Differences in the expression profiles of miRNAs and mRNAs have been reported in colorectal cancer. Nevertheless, information on important miRNA-mRNA regulatory modules in colorectal cancer is still lacking. In this regard, this study presents an application of the RH-SAC algorithm on miRNA and mRNA expression data for identification of potential miRNA-mRNA modules. First, a set of miRNA rules was generated using the RH-SAC algorithm. The mRNA targets of the selected miRNAs were identified using the miRTarBase database. Next, the expression values of target mRNAs were used to generate mRNA rules using the RH-SAC. Then all miRNA-mRNA rules have been integrated for generating networks. The RH-SAC algorithm unlike other existing methods selects a group of co-expressed miRNAs and mRNAs that are also differentially expressed. In total 17 miRNAs and 141 mRNAs were selected. The enrichment analysis of selected mRNAs revealed that our method selected mRNAs that are significantly associated with colorectal cancer. We identified novel miRNA/mRNA interactions in colorectal cancer. Through experiment, we could confirm that one of our discovered miRNAs, hsa-miR-93-5p, was significantly up-regulated in 75.8% CRC in comparison to their corresponding non-tumor samples. It could have the potential to examine colorectal cancer subtype specific unique miRNA/mRNA interactions.
authors.affiliation: Department of Bioscience &Bioengineering, Indian Institute of Technology Jodhpur, India.
authors.forename: Sushmita
authors.initials: S
authors.lastname: Paul
authors.affiliation: Experimental Tumorpathology, Institute of Pathology, University Hospital of Friedrich-Alexander-University Erlangen-Nürnberg, Germany.
authors.forename: Petra
authors.initials: P
authors.lastname: Lakatos
authors.affiliation: Institute of Pathology, University Hospital of Friedrich-Alexander-University Erlangen-Nürnberg, Germany.
authors.forename: Arndt
authors.initials: A
authors.lastname: Hartmann
authors.affiliation: Experimental Tumorpathology, Institute of Pathology, University Hospital of Friedrich-Alexander-University Erlangen-Nürnberg, Germany.
authors.forename: Regine
authors.initials: R
authors.lastname: Schneider-Stock
authors.affiliation: Laboratory of Systems Tumor Immunology, Department of Dermatology, Erlangen University Hospital and Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
authors.forename: Julio
authors.initials: J
authors.lastname: Vera
mesh_terms: D016000:Cluster Analysis; D015179:Colorectal Neoplasms / Q000235:genetics / Q000401:mortality / Q000473:pathology*; D030541:Databases, Genetic; D053263:Gene Regulatory Networks; D006801:Humans; D053208:Kaplan-Meier Estimate; D035683:MicroRNAs / Q000378:metabolism*; D011379:Prognosis; D012333:RNA, Messenger / Q000378:metabolism*; D060388:Support Vector Machine; D059467:Transcriptome; D015854:Up-Regulation
chemical_list: C543350:MIRN93 microRNA, human; D035683:MicroRNAs; D012333:RNA, Messenger