Online Tools

LncPriCNet – Global Prioritizing Disease Candidate lncRNAs via a Multi-level Composite Network

lncRNA

LncRNAs play pivotal roles in many important biological processes, but research on the functions of lncRNAs in human disease is still in its infancy. Therefore, it is urgent to prioritize lncRNAs that are potentially associated with diseases. Researchers from the Shanghai Jiao Tong University have developed a novel algorithm, LncPriCNet, that uses a multi-level composite network to prioritize candidate lncRNAs ...

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Urb-RIP – An Adaptable and Efficient Approach for Immunoprecipitation of lncRNAs and Associated RNAs/Proteins

Post-transcriptional regulation of gene expression is an important process that is mediated by interactions between mRNAs and RNA binding proteins (RBP), non-coding RNAs (ncRNA) or ribonucleoproteins (RNP). Key to the study of post-transcriptional regulation of mRNAs and the function of ncRNAs such as long non-coding RNAs (lncRNAs) is an understanding of what factors are interacting with these transcripts. While several ...

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Slncky – evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs

lncRNA

Recent advances in transcriptome sequencing have enabled the discovery of thousands of long non-coding RNAs (lncRNAs) across many species. Though several lncRNAs have been shown to play important roles in diverse biological processes, the functions and mechanisms of most lncRNAs remain unknown. Two significant obstacles lie between transcriptome sequencing and functional characterization of lncRNAs: identifying truly non-coding genes from de ...

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AnnoLnc – a web server for systematically annotating novel human lncRNAs

lncRNA

Long noncoding RNAs (lncRNAs) have been shown to play essential roles in almost every important biological process through multiple mechanisms. Although the repertoire of human lncRNAs has rapidly expanded, their biological function and regulation remain largely elusive, calling for a systematic and integrative annotation tool. Here researchers from Peking University present AnnoLnc, a one-stop portal for systematically annotating novel human ...

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DeepLNC, a long non-coding RNA prediction tool using a deep neural network

lncRNA

The significant role of long non-coding RNAs (lncRNAs) in various cellular functions, such as gene imprinting, immune response, embryonic pluripotency, tumorogenesis, and genetic regulations, has been widely studied and reported in recent years. Several experimental and computational methods involving genome-wide search and screenings of ncRNAs are being proposed utilizing sequence features-length, occurrence, and composition of bases with various limitations. Researchers ...

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spongeScan – a graphical web tool for detecting microRNA binding elements in lncRNA sequences

lncRNA

Non-coding RNA transcripts such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are important genetic regulators. However, the functions of many of these transcripts are still not clearly understood. Recently, it has become apparent that there is significant crosstalk between miRNAs and lncRNAs and that this creates competition for binding between the miRNA, a lncRNA and other regulatory targets. Indeed, ...

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LncRNA2Function – a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data

lncRNA

The GENCODE project has collected over 10,000 human long non-coding RNA (lncRNA) genes. However, the vast majority of them remain to be functionally characterized. Computational investigation of potential functions of human lncRNA genes is helpful to guide further experimental studies on lncRNAs. In this study, based on expression correlation between lncRNAs and protein-coding genes across 19 human normal tissues, researchers ...

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REDItools – Uncovering RNA Editing Sites in Long Non-Coding RNAs

lncRNA

RNA editing is an important co/post-transcriptional molecular process able to modify RNAs by nucleotide insertions/deletions or substitutions. In human, the most common RNA editing event involves the deamination of adenosine (A) into inosine (I) through the adenosine deaminase acting on RNA proteins. Although A-to-I editing can occur in both coding and non-coding RNAs, recent findings, based on RNA-seq experiments, have ...

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TF2LncRNA: Identifying Common Transcription Factors for a List of lncRNA Genes from ChIP-Seq Data

lncrna

High-throughput genomic technologies like lncRNA microarray and RNA-Seq often generate a set of lncRNAs of interest, yet little is known about the transcriptional regulation of the set of lncRNA genes. Here, based on ChIP-Seq peak lists of transcription factors (TFs) from ENCODE and annotated human lncRNAs from GENCODE, researchers from the Harbin Institute of Technology have developed a web-based interface ...

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Systematically profiling and annotating long intergenic non-coding RNAs in human embryonic stem cell

lncRNA

While more and more long intergenic non-coding RNAs (lincRNAs) were identified to take important roles in both maintaining pluripotency and regulating differentiation, how these lincRNAs may define and drive cell fate decisions on a global scale are still mostly elusive. Systematical profiling and comprehensive annotation of embryonic stem cells lincRNAs may not only bring a clearer big picture of these ...

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