Methods

LncRNAs2Pathways – Identifying the pathways influenced by a set of lncRNAs of interest based on a global network propagation method

Long non-coding RNAs (lncRNAs) have been demonstrated to play essential roles in diverse cellular processes and biological functions. Exploring the functions associated with lncRNAs may help provide insight into their underlying biological mechanisms. The current methods primarily focus on investigating the functions of individual lncRNAs; however, essential biological functions may be affected by the combinatorial effects of multiple lncRNAs. Here, ...

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ASSA – Transcriptome-Wide Prediction Of lncRNA-RNA Interactions By Thermodynamics

lncRNA

The discovery of thousands of long noncoding RNAs (lncRNAs) in mammals raises a question about their functionality. It has been shown that some of them function post-transcriptionally via formation of inter-molecular duplexes. Sequence alignment tools are frequently used for transcriptome-wide prediction of RNA-RNA interactions. However, such approaches have poor prediction accuracy since they ignore RNA secondary structure and interaction energy. ...

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LncFunNet – an integrated computational framework for identification of functional long noncoding RNAs

lncRNA

Long noncoding RNAs (lncRNAs) are key regulators of diverse cellular processes. Recent advances in high-throughput sequencing have allowed for an unprecedented discovery of novel lncRNAs. To identify functional lncRNAs from thousands of candidates for further functional validation is still a challenging task. Here, researchers from the Chinese University of Hong Kong present a novel computational framework, lncFunNet (lncRNA Functional inference ...

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Exploring functions of long noncoding RNAs across multiple cancers through co-expression network

lncrna

In contrast to protein-coding genes, long-noncoding RNAs (lncRNAs) are much less well understood, despite increasing evidence indicating a wide range of their biological functions, and possible roles in various cancers. Based on public RNA-seq datasets of four solid cancer types, researchers from Sichuan University utilize Weighted Correlation Network Analysis (WGCNA) to propose a strategy for exploring the functions of lncRNAs ...

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Lncident – A Tool for Rapid Identification of Long Noncoding RNAs

lncrna

More and more studies have demonstrated that long noncoding RNAs (lncRNAs) play critical roles in diversity of biological process and are also associated with various types of disease. How to rapidly identify lncRNAs and messenger RNA is the fundamental step to uncover the function of lncRNAs identification. Researchers at Jilin University have devloped a novel method for rapid identification of ...

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IntNetLncSim – an integrative network analysis method to infer human lncRNA functional similarity

Increasing evidence indicated that long non-coding RNAs (lncRNAs) were involved in various biological processes and complex diseases by communicating with mRNAs/miRNAs each other. Exploiting interactions between lncRNAs and mRNA/miRNAs to lncRNA functional similarity (LFS) is an effective method to explore function of lncRNAs and predict novel lncRNA-disease associations. Researchers from Harbin Medical University have proposed an integrative framework, IntNetLncSim, to ...

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Researchers develop new CRISPR sgRNA design tool, demonstrate efficient CRISPR deletion of an enhancer and exonic fragment of the lncRNA MALAT1

lncRNA

CRISPR-Cas9 technology can be used to engineer precise genomic deletions with pairs of single guide RNAs (sgRNAs). This approach has been widely adopted for diverse applications, from disease modelling of individual loci, to parallelized loss-of-function screens of thousands of regulatory elements. However, no solution has been presented for the unique bioinformatic design requirements of CRISPR deletion. Researchers from the Centre for ...

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Bioinformatics for Novel Long Intergenic Noncoding RNA (lincRNA) Identification

lncRNA

Long intergenic noncoding RNAs (lincRNAs) , which are larger than 200 nucleotides and transcribed from the intergenic regions of protein coding genes, have been shown by accumulating findings to be widely expressed and extensively functional in many cellular processes. Nevertheless, given their cell/tissue-specificity, there is a need of identifying novel lincRNAs in a given system. To fulfill this purpose, researchers ...

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New tool predicts the interaction of proteins and RNA

CRG Researchers developed Global Score, a method that allows, for the first time, to predict protein interactions with long non-coding RNAs. This algorithm helps scientists prioritize binding partners for experimental validation, which will contribute to our understanding of the role of long non-coding RNAs in normal cell function and in disease. Far from just reading the information contained in the ...

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High-throughput annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing (CLS)

lncrna

Accurate annotations of genes and their transcripts is a foundation of genomics, but no annotation technique presently combines throughput and accuracy. As a result, current reference gene collections remain far from complete: many genes models are fragmentary, while thousands more remain uncatalogued, particularly for long non coding RNAs (lncRNAs). To accelerate lncRNA annotation, the GENCODE consortium has developed RNA Capture ...

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