TransmiR v3.0: an updated transcription factor-microRNA regulation database

Nucleic Acids Res. 2024 Nov 12:gkae1081. doi: 10.1093/nar/gkae1081. Online ahead of print.

ABSTRACT

microRNAs (miRNAs) are active in various biological processes by mediating gene expression, and the full investigation of miRNA transcription is crucial for understanding the mechanisms underlying miRNA deregulation in pathological conditions. Here an updated TransmiR v3.0 database is presented with more comprehensive miRNA transcription regulation information, which contains 5095 transcription factor (TF) -miRNA regulations curated from 2285 papers and >6 million TF-miRNA regulations derived from ChIP-seq data. Currently, TransmiR v3.0 covers 3260 TFs, 4253 miRNAs and 514 433 TF-miRNA regulation pairs across 29 organisms. Additionally, motif scanning of TF loci on promoter sequences of miRNAs from multiple species is employed to predict TF-miRNA regulations, generating 284 527 predicted TF-miRNA regulations. Besides the significant growth of data volume, we also improve the annotations for TFs and miRNAs by introducing the TF family, TFBS motif, and expression profiles for several species. Moreover, the functionality of the TransmiR v3.0 online database is enhanced, including allowing batch search for flexible queries and offering more extensive disease-specific, as well as newly sex-specific TF-miRNA regulation networks in the 'Network' module. TransmiR v3.0 provides a useful resource for studying miRNA biogenesis regulation and can be freely accessed at http://www.cuilab.cn/transmir.

PMID:39530226 | DOI:10.1093/nar/gkae1081