lnCeDB: database of human long noncoding RNA acting as competing endogenous RNA

Area of Science:

• Molecular Biology
• Genomics
• Bioinformatics

Background:

• Long noncoding RNAs (lncRNAs) play a role in post-transcriptional gene regulation.
• lncRNAs can function as competing endogenous RNAs (ceRNAs) by interacting with microRNAs (miRNAs).
• This interaction influences miRNA availability for binding to target messenger RNAs (mRNAs), thereby affecting gene expression.

Purpose of the Study:

• To establish a comprehensive database, lnCeDB, for human long noncoding RNAs.
• To identify potential ceRNA interactions between lncRNAs and mRNAs.
• To provide tools for analyzing the likelihood of these ceRNA interactions.

Main Methods:

• Collected human lncRNA data from GENCODE version 19.
• Integrated miRNA target data from TargetScan and StarBase.
• Predicted miRNA targets on lncRNAs using a seed-matching algorithm.
• Developed a ceRNA score and hypergeometric test for interaction likelihood.
• Incorporated expression data across 22 human tissues.

Main Results:

• lnCeDB provides a curated collection of human lncRNAs with potential ceRNA activity.
• The database includes predicted miRNA-lncRNA and miRNA-mRNA interactions.
• Tools are available to calculate ceRNA scores and P-values for interaction pairs.
• Tissue-specific expression data aids in assessing the biological relevance of ceRNA pairs.

Conclusions:

• lnCeDB serves as a valuable resource for exploring lncRNA-mediated gene regulation.
• The database facilitates the identification and validation of ceRNA networks.
• lnCeDB aids researchers in understanding the functional roles of lncRNAs in various biological processes.