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miRNA Binding Site

PARma

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

PARma is a complete data analysis software for AGO-PAR-CLIP experiments to identify target sites of microRNAs as well as the microRNA binding to these sites. It integrates specific characteristics of the experiments into a generative model. The model and a novel pattern discovery tool are iteratively applied to data to estimate seed activity probabilities, cluster confidence scores and to assign the most probable microRNA. Based on differential PAR-CLIP analysis and comparison to RIP-Chip data, we show that PARma is more accurate than existing approaches.

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miRModule

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MicroRNAs (miRNAs) play critical roles in gene regulation. Although it is well known that multiple miRNAs may work as miRNA modules to synergistically regulate common target mRNAs, the understanding of miRNA modules is still in its infancy.

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miRTCat

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MicroRNAs (miRNAs) regulate various biological functions by binding hundreds of transcripts to impart post-transcriptional repression. Recently, by applying a transcriptome-wide experimental method for identifying miRNA target sites (Ago HITS-CLIP), a novel non-canonical target site, named 'nucleation bulge', was discovered as widespread, functional and evolutionally conserved. Although such non-canonical nucleation bulges have been proven to be predictive by using 'pivot pairing rule' and sequence conservation, this approach has not been applied yet.

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miREE

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

Computational methods for microRNA target prediction are a fundamental step to understand the miRNA role in gene regulation, a key process in molecular biology. In this paper we present miREE, a novel microRNA target prediction tool. miREE is an ensemble of two parts entailing complementary but integrated roles in the prediction. The Ab-Initio module leverages upon a genetic algorithmic approach to generate a set of candidate sites on the basis of their microRNA-mRNA duplex stability properties.

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SNPinfo

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

We have developed a set of web-based SNP selection tools (freely available at http://www.niehs.nih.gov/snpinfo) where investigators can specify genes or linkage regions and select SNPs based on GWAS results, linkage disequilibrium (LD), and predicted functional characteristics of both coding and non-coding SNPs. The algorithm uses GWAS SNP P-value data and finds all SNPs in high LD with GWAS SNPs, so that selection is from a much larger set of SNPs than the GWAS itself.

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TriplexRna

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MicroRNAs (miRNAs) are an integral part of gene regulation at the post-transcriptional level. Recently, it has been shown that pairs of miRNAs can repress the translation of a target mRNA in a cooperative manner, which leads to an enhanced effectiveness and specificity in target repression. However, it remains unclear which miRNA pairs can synergize and which genes are target of cooperative miRNA regulation.

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miRTar Hunter

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MicroRNAs (miRNAs) are important regulators of gene expression and play crucial roles in many biological processes including apoptosis, differentiation, development, and tumorigenesis. Recent estimates suggest that more than 50% of human protein coding genes may be regulated by miRNAs and that each miRNA may bind to 300-400 target genes. Approximately 1,000 human miRNAs have been identified so far with each having up to hundreds of unique target mRNAs.

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MtiBase

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MicroRNAs (miRNAs) play an important role in the regulation of gene expression. Previous studies on miRNA functions mainly focused on their target sites in the 3' untranslated regions (UTRs) of mRNAs. However, increasing evidence has revealed that miRNAs can also induce mRNA degradation and mediate translational repression via complementary interactions with the coding sequence (CDS) and 5'UTR of mRNAs.

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GeneACT

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

Deciphering gene regulatory networks requires the systematic identification of functional cis-acting regulatory elements. We present a suite of web-based bioinformatics tools, called GeneACT http://promoter.colorado.edu, that can rapidly detect evolutionarily conserved transcription factor binding sites or microRNA target sites that are either unique or over-represented in differentially expressed genes from DNA microarray data.

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VARIANT

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

The massive use of Next-Generation Sequencing (NGS) technologies is uncovering an unexpected amount of variability. The functional characterization of such variability, particularly in the most common form of variation found, the Single Nucleotide Variants (SNVs), has become a priority that needs to be addressed in a systematic way.

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