Web Based Tools

TargetScan7.1 Mouse Released

by Christoph on February 3, 2016

in Web Based Tools

TargetScan Mouse Release 7.1 - Prediction of miRNA targets in mouseThe TargetScan team is excited to announce the official release of the next generation of their microRNA (miRNA) target prediction resource: TargetScan7.1 for the mouse species which can be accessed at http://www.targetscan.org/mmu_71/ . It is a follow-up resource to their paper on major improvements to miRNA target prediction algorithms, published in August 2015 (http://elifesciences.org/content/4/e05005/), and a follow-up to the previously released TargetScan7.0 for the Human. This latest release features

  • heavily revised 3′ UTR annotations,
  • updated evolutionary information encompassing an expanded repertoire of mammalian species,
  • improvements in the usage of features predictive of effective miRNA target sites,
  • improved miRNA conservation classifications for miRNA families,
  • enhanced user interface that simplifies data accessibility.

The authors are looking forward to hear any feedback regarding the website as they are “determined to further improve the resource for the miRNA community.

 

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DASHR: database of small human noncoding RNAsDescription:  Small non-coding RNAs (sncRNAs) are highly abundant RNAs, typically <100 nucleotides long, that act as key regulators of diverse cellular processes. Although thousands of sncRNA genes are known to exist in the human genome, no single database provides searchable, unified annotation, and expression information for full sncRNA transcripts and mature RNA products derived from these larger RNAs. Here, we present the Database of small human noncoding RNAs (DASHR). DASHR contains the most comprehensive information to date on human sncRNA genes and mature sncRNA products. DASHR provides a simple user interface for researchers to view sequence and secondary structure, compare expression levels, and evidence of specific processing across all sncRNA genes and mature sncRNA products in various human tissues. DASHR annotation and expression data covers all major classes of sncRNAs including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear, nucleolar, cytoplasmic (sn-, sno-, scRNAs, respectively), transfer (tRNAs), and ribosomal RNAs (rRNAs). Currently, DASHR (v1.0) integrates 187 smRNA high-throughput sequencing (smRNA-seq) datasets with over 2.5 billion reads and annotation data from multiple public sources. DASHR contains annotations for ∼48 000 human sncRNA genes and mature sncRNA products, 82% of which are expressed in one or more of the curated tissues. DASHR is available at http://lisanwanglab.org/DASHR.

Newly published in the Nucleic Acid Research Database issue:
http://www.ncbi.nlm.nih.gov/pubmed/26553799

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MirGeneDB logoMicroRNAs (miRNAs) are a novel class of gene regulators that are now the center of their own research field in human cancer: the non-coding RNA field. MiRNAs are ~22nt long non-coding RNA transcripts that derive from hairpin precursors and regulate gene-expression of target genes by inhibiting the protein production of the target genes’ messenger RNA (Jonas and Izaurralde 2015; Lin and Gregory 2015). Although much is known about miRNAs, with now nearly 40’000 scientific articles written about them alone, paradoxically defining what is and what is not a miRNA has been difficult, severely hampering studies on their potential roles in cancer, for example.

In order to enable researchers to accurately study the dynamics of the human miRNA landscape, an international  group under the lead of Professor Kevin J. Peterson (Dartmouth, US) and Dr. Bastian Fromm (Oslo, Norway) decided to revisit the available human miRNA complement (Kozomara and Griffiths-Jones 2014). Fromm et al established and then applied a set of consistent criteria for the annotation of miRNAs. This set was derived from numerous recent publications that elucidated details of miRNA maturation/processing in the cell (Auyeung, et al. 2013; Schirle and MacRae 2012; Schirle, et al. 2014a; Schirle, et al. 2014b; Seitz, et al. 2008; Suzuki, et al. 2015; Tsutsumi, et al. 2011). They show that less than a third of the 1,881 human miRBase entries are robustly supported as the products of miRNA genes. These robustly supported 523 human miRNA genes sequences are [click to continue…]

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miRWalk 2.0 available

by Christoph on December 2, 2014

in Software, Web Based Tools

miRWalk-2-logomiRWalk2.0 (http://zmf.umm.uni-heidelberg.de/apps/zmf/mirwalk2/) which is a significantly improved and upgraded version of miRWalk database is now available for the scientific community.

miRWalk2.0 was developed with the aim of providing a regularly updated, freely accessible, comprehensive archive to supply the biggest available collection of predicted and experimentally verified miRNA-target interactions with various novel and unique features to greatly assist the scientific community. About 858,750,070 interactions between 11,748 miRNAs and 308,700 genes are documented in miRWalk2.0 with 5,077,757 different kinds of identifiers to offer a one-stop site to collect an abundance of information.

miRWalk2.0 not only documents miRNA binding sites within the complete sequence of a gene, but also combines this information with a comparison of binding sites [click to continue…]

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mrSNP workflowmrSNP is a highly adaptable and performing web based tool for predicting the effect a 3’UTR SNP will have on miRNA binding. This tool has advantages over existing algorithms because it can assess the effect of novel SNPs on miRNA binding without requiring significant hands on time.

Project home page: http://mrsnp.osu.edu
License: Free for commercial and academic use

Background

MicroRNAs (miRNAs) bind to sites in the 3’untranslated regions (3’UTR) of a targeted messenger RNA (mRNA). Binding leads to degradation of the transcript or blocked translation resulting in decreased expression of the targeted gene. Single nucleotide polymorphisms (SNPs) have been found in 3’UTRs that disrupt normal miRNA binding or introduce new binding sites and some of these have been associated with disease pathogenesis. This raises the importance of detecting miRNA targets and [click to continue…]

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starBase update: deciphering Pan-Cancer patterns of miRNAs, lncRNAs, ceRNAs and RNA-binding proteins from TCGA 14 cancer types

February 8, 2014

StarBase has been updated to explore Pan-Cancer pattern of lncRNAs, miRNAs, RNA-binding proteins (RBP) and their regulatory networks (ceRNA, coexpression) by mining expression profiles of miRNAs, lncRNAs and mRNAs across 14 cancer types (>6000 samples) from The Cancer Genome Atlas (TCGA) Data Portal (all data available without limitations). StarBase provides the following Pan-Cancer Analysis Services: […]

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ChIPBase: decoding the transcriptional regulation of microRNA and lncRNA genes from ChIP-Seq data

November 28, 2012

microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) and represent two classes of important non-coding RNAs in eukaryotes. Although these non-coding RNAs have been implicated in organismal development and in various human diseases, surprisingly little is known about their transcriptional regulation. Recent advances in chromatin immunoprecipitation with next-generation DNA sequencing (ChIP-Seq) have provided methods of detecting […]

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miREC: Database of miRNAs involved in endometrial cancer

September 19, 2012

The miREC database (miRNAs involved in Endometrial Cancer) combines published data about miRNAs and genes deregulated in endometrial cancer, as well as target-regulator relationships between these genes and miRNAs. All information has been extracted from published literature and entries are supplemented by reference citations. The miREC database was launched in February 2011  by researchers at […]

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miRandola – Extracellular/Circulating microRNAs Database

September 9, 2012

With two miRNA conferences coming up that focus on this field I thought the following manually curated database will be useful: miRandola. Extracellular miRNAs in serum, plasma, saliva, urine and other body fluids have recently been shown to be associated with various pathological conditions including cancer. miRNAs circulate in the bloodstream in a highly stable, […]

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miRviewer: A multispecies microRNA homologous viewer

February 16, 2012

In order to better understand microRNAs of interest it is of utmost importance to learn about the genomic conservation of these genes. The miRviewer web-server encompasses all known (and some novel) microRNAs of currently fully annotated animal genomes in a visual ‘birds-eye’ view representation. miRviewer provides a graphical outlook of the current microRNA world together […]

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