Dataset for regulation between lncRNAs and their nearby protein-coding genes in human cancers

This article contains data related to the research article entitled Systematic analysis reveals long noncoding RNAs regulating neighboring transcription factors in human cancers (Liu et al., 2018 in press) [1]. Long noncoding RNAs (IncRNAs) are proposed to play essential roles in modulating the expression of the nearby loci. In this study, we systematically investigated the relationship between IncRNAs and their neighboring genes based on the genomic location of genes and the transcriptome expression profiles from TCGA samples across 12 tumor types. Position conservation analysis was applied to find IncRNAs conserved by position across vertebrate species. Gene ontology and enrichment analysis identified TF genes as a specific type of protein-coding genes that adjacent to highly positionally conserved IncRNA. The expression correlation of IncRNAs and their adjacent TFs were assessed across tumors to define significant co-expressed IncRNA-TF pairs, and a causal inference test (CIT) was used to infer the causal regulation of IncRNA on its nearby TF genes. A list of candidate IncRNA/TF regulation pairs in tumors was provided. (C) 2018 The Authors. Published by Elsevier Inc.