title: mirCoX: a database of miRNA-mRNA expression correlations derived from RNA-seq meta-analysis.
abstract: BACKGROUND
  Experimentally validated co-expression correlations between miRNAs and genes are a valuable resource to corroborate observations about miRNA/mRNA changes after experimental perturbations, as well as compare miRNA target predictions with empirical observations. For example, when a given miRNA is transcribed, true targets of that miRNA should tend to have lower expression levels relative to when the miRNA is not expressed.
  
  
  METHODS
  We processed publicly available human RNA-seq experiments obtained from NCBI's Sequence Read Archive (SRA) to identify miRNA-mRNA co-expression trends and summarized them in terms of their Pearson's Correlation Coefficient (PCC) and significance.
  
  
  RESULTS
  We found that sequence-derived parameters from TargetScan and miRanda were predictive of co-expression, and that TargetScan- and miRanda-derived gene-miRNA pairs tend to have anti-correlated expression patterns in RNA-seq data compared to controls. We provide this data for download and as a web application available at http://wrenlab.org/mirCoX/.
  
  
  CONCLUSIONS
  This database of empirically established miRNA-mRNA transcriptional correlations will help to corroborate experimental observations and could be used to help refine and validate miRNA target predictions.
authors.forename: Cory B
authors.initials: CB
authors.lastname: Giles
authors.forename: Reshmi
authors.initials: R
authors.lastname: Girija-Devi
authors.forename: Mikhail G
authors.initials: MG
authors.lastname: Dozmorov
authors.forename: Jonathan D
authors.initials: JD
authors.lastname: Wren
mesh_terms: D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D030561:Databases, Nucleic Acid; D015870:Gene Expression; D020869:Gene Expression Profiling; D006801:Humans; D020407:Internet; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger