title: From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data.
abstract: RNA-Seq techniques generate hundreds of millions of short RNA reads using next-generation sequencing (NGS). These RNA reads can be mapped to reference genomes to investigate changes of gene expression but improved procedures for mining large RNA-Seq datasets to extract valuable biological knowledge are needed. RNAMiner--a multi-level bioinformatics protocol and pipeline--has been developed for such datasets. It includes five steps: Mapping RNA-Seq reads to a reference genome, calculating gene expression values, identifying differentially expressed genes, predicting gene functions, and constructing gene regulatory networks. To demonstrate its utility, we applied RNAMiner to datasets generated from Human, Mouse, Arabidopsis thaliana, and Drosophila melanogaster cells, and successfully identified differentially expressed genes, clustered them into cohesive functional groups, and constructed novel gene regulatory networks. The RNAMiner web service is available at http://calla.rnet.missouri.edu/rnaminer/index.html.
authors.affiliation: Computer Science Department, University of Missouri, Columbia, Missouri, United States of America; MU Botanical Center, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Jilong
authors.initials: J
authors.lastname: Li
authors.affiliation: Computer Science Department, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Jie
authors.initials: J
authors.lastname: Hou
authors.affiliation: Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Lin
authors.initials: L
authors.lastname: Sun
authors.affiliation: Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Jordan Maximillian
authors.initials: JM
authors.lastname: Wilkins
authors.affiliation: MU Botanical Center, University of Missouri, Columbia, Missouri, United States of America; Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Lu
authors.affiliation: Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Chad E
authors.initials: CE
authors.lastname: Niederhuth
authors.affiliation: Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Benjamin Ryan
authors.initials: BR
authors.lastname: Merideth
authors.affiliation: Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Thomas P
authors.initials: TP
authors.lastname: Mawhinney
authors.affiliation: MU Botanical Center, University of Missouri, Columbia, Missouri, United States of America; Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Valeri V
authors.initials: VV
authors.lastname: Mossine
authors.affiliation: MU Botanical Center, University of Missouri, Columbia, Missouri, United States of America; Department of Chemistry, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: C Michael
authors.initials: CM
authors.lastname: Greenlief
authors.affiliation: Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: John C
authors.initials: JC
authors.lastname: Walker
authors.affiliation: MU Botanical Center, University of Missouri, Columbia, Missouri, United States of America; Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: William R
authors.initials: WR
authors.lastname: Folk
authors.affiliation: MU Botanical Center, University of Missouri, Columbia, Missouri, United States of America; Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Mark
authors.initials: M
authors.lastname: Hannink
authors.affiliation: MU Botanical Center, University of Missouri, Columbia, Missouri, United States of America; Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Dennis B
authors.initials: DB
authors.lastname: Lubahn
authors.affiliation: Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: James A
authors.initials: JA
authors.lastname: Birchler
authors.affiliation: Computer Science Department, University of Missouri, Columbia, Missouri, United States of America; MU Botanical Center, University of Missouri, Columbia, Missouri, United States of America; Informatics Institute, University of Missouri, Columbia, Missouri, United States of America; C. Bond Life Science Center, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Jianlin
authors.initials: J
authors.lastname: Cheng
mesh_terms: D000818:Animals; D017360:Arabidopsis / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining; D030541:Databases, Genetic; D004331:Drosophila melanogaster / Q000235:genetics; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D016678:Genome; D006801:Humans; D020407:Internet; D051379:Mice; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D013223:Statistics as Topic