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

Abstract

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 (lncRNAs) are proposed to play essential roles in modulating the expression of the nearby loci. In this study, we systematically investigated the relationship between lncRNAs 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 lncRNAs 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 lncRNA. The expression correlation of lncRNAs and their adjacent TFs were assessed across tumors to define significant co-expressed lncRNA-TF pairs, and a causal inference test (CIT) was used to infer the causal regulation of lncRNA on its nearby TF genes. A list of candidate lncRNA/TF regulation pairs in tumors was provided.

LINC00511 is associated with the malignant status and promotes cell proliferation and motility in cervical cancer

“…Long noncoding RNAs (lncRNAs) are considered a type of non-coding RNAs consisting of more than 200 nucleotides without coding protein potential [10]. More and more researches suggested lncRNAs are involved in human cancer development by regulating tumor cell proliferation, apoptosis, cell-cycle, migration, invasion, and autophagy [11,12]. Long intergenic noncoding RNA 00511 (LINC00511, also known as onco-lncRNA-12), is a newly identified carcinogenic lncRNA that maps to chromosome 17q24.3 [13].…”

LncRNA TMPO‐AS1 promotes LCN2 transcriptional activity and exerts oncogenic functions in ovarian cancer

“…LncRNAs are well acknowledged to mediate gene transcription and recent research attention has been attracted to their implication in tumorigenesis due to their crosstalk with neighboring transcription factor genes 25,26. In our study, we found that lncRNA TMPO‐AS1 could bind to E2F6 to interrupt the binding between E2F6 and LCN2, by which the LCN2 expression was activated.…”

“…Measurement data (mean ± standard deviation) among multiple groups were assessed by one-way ANOVA, followed by Tukey's post hoc test and those in relation to time-based measurements within each group were assessed by repeated measures ANOVA, followed by Tukey's post hoc test neighboring transcription factor genes. 25,26 In our study, we found that lncRNA TMPO-AS1 could bind to E2F6 to interrupt the binding between E2F6 and LCN2, by which the LCN2 expression was activated. Similar transcription factor-associated lncRNAs mechanism has been validated in connection with overall survival, disease-free survival, and progression-free survival of patients with ovarian cancer.…”

DARS-AS1 recruits METTL3/METTL14 to bind and enhance DARS mRNA m 6 A modification and translation for cytoprotective autophagy in cervical cancer

“…LncRNAs are proposed to play essential roles in regulating the expression of the nearby loci [ 38 ]. To probe the interaction between DARS-AS1 and its nearby gene DARS in CC, we first employed GEPIA 2 database to analyse the correlation between their expression in CC tissues.…”