Lnc2Catlas: an atlas of long noncoding RNAs associated with risk of cancers

Abstract

Lnc2Catlas (http://lnc2catlas.bioinfotech.org/) is an atlas of long noncoding RNAs (lncRNAs) associated with cancer risk. LncRNAs are a class of functional noncoding RNAs with lengths over 200 nt and play a vital role in diverse biological processes. Increasing evidence shows that lncRNA dysfunction is associated with many human cancers/diseases. It is therefore important to understand the underlying relationship between lncRNAs and cancers. To this end, we developed Lnc2Catlas to compile quantitative associations between lncRNAs and cancers using three computational methods, assessing secondary structure disruption, lncRNA-protein interactions, and co-expression networks. Lnc2Catlas was constructed based on 27,670 well-annotated lncRNAs, 31,749,216 SNPs, 1,473 cancer-associated proteins, and 10,539 expression profiles of 33 cancers from The Cancer Genome Atlas (TCGA). Lnc2Catlas contains 247,124 lncRNA-SNP pairs, over two millions lncRNA-protein interactions, and 6,902 co-expression clusters. We deposited Lnc2Catlas on Alibaba Cloud and developed interactive, mobile device-compatible, user-friendly interfaces to help users search and browse Lnc2Catlas with ultra-low latency. Lnc2Catlas can aid in the investigation of associations between lncRNAs and cancers and can provide candidate lncRNAs for further experimental validation. Lnc2Catlas will facilitate an understanding of the associations between lncRNAs and cancer and will help reveal the critical role of lncRNAs in cancer.

The how and why of lncRNA function: An innate immune perspective

“…There are several databases that summarize the plethora of published human sequencing studies, including UK Biobank [107] and GWAS Catalog -EMBL-EBI [108]. Other databases specifically focus on SNPs within lncRNAs, such as lncRNASNP2 [109] and Lnc2Catlas [110].…”

“…Both of these studies started by investigating clinically relevant SNPs that led to the discovery of disease-associated lncRNAs, providing the groundwork for future studies on potential biomarkers or the development of novel therapeutic targets for a variety of inflammatory diseases. Additionally, as previously mentioned, XENA or Lnc2Catlas are databases that combine RNA sequencing of tissue samples from healthy and cancer patients, these tools can also be adapted to assess age, gender, tissue or even disease association of splice variants [98,110]. These disease-associated SNPs or splice variants will help guide further studies to determine therapeutic or biomarker potential.…”

Long non-coding RNAs (lncRNAs) in spermatogenesis and male infertility

“…It provides association between 33 different cancers and 27,670 lncRNA transcripts. Human Lnc2catlas.bioinfotech.org [ 93 ] LncRIsearch It is a web server which predicts human and mouse lncRNA-lncRNA and lncRNA-mRNA interactions. It uses RI blast to predict RNA-RNA interaction.…”

The Interplay between Long Noncoding RNAs and Proteins of the Epigenetic Machinery in Ovarian Cancer

“…Other databases were specially built to provide information on lncRNA-disease associations, such as LncRNADisease, Lnc2Cancer, MNDR, ncRPheno, and Lnc2Catlas [123,125,[127][128][129]. LncRNADisease combines experimental and bioinformatic evidence to provide information on relationships between lncRNAs or circRNAs and diseases.…”