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miRHiC

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

MicroRNAs (miRNAs), a class of endogenous small regulatory RNAs, play important roles in many biological and physiological processes. The perturbations of some miRNAs, which are usually called as onco-microRNAs (onco-miRs), are significantly associated with multiple stages of cancer. Although hundreds of miRNAs have been discovered, the perturbed miRNA regulatory networks and their functions are still poorly understood in cancer. Analyzing the expression patterns of miRNA target genes is a very useful strategy to infer the perturbed miRNA networks.

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MirPlex

Submitted by ChenLiang on Sun, 09/10/2017 - 20:27

MicroRNAs (miRNAs) are a class of small non-coding RNA (sRNA) involved in gene regulation through mRNA decay and translational repression. In animals, miRNAs have crucial regulatory functions during embryonic development and they have also been implicated in several diseases such as cancer, cardiovascular and neurodegenerative disorders. As such, it is of importance to successfully characterize new miRNAs in order to further study their function.

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HomoTarget

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

MiRNAs play an essential role in the networks of gene regulation by inhibiting the translation of target mRNAs. Several computational approaches have been proposed for the prediction of miRNA target-genes. Reports reveal a large fraction of under-predicted or falsely predicted target genes. Thus, there is an imperative need to develop a computational method by which the target mRNAs of existing miRNAs can be correctly identified.

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PlantMirnaT

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

miRNA is known to regulate up to several hundreds coding genes, thus the integrated analysis of miRNA and mRNA expression data is an important problem. Unfortunately, the integrated analysis is challenging since it needs to consider expression data of two different types, miRNA and mRNA, and target relationship between miRNA and mRNA is not clear, especially when microarray data is used.

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RandA

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

Non-coding RNAs (ncRNA) account for a large portion of the transcribed genomic output. This diverse family of untranslated RNA molecules play a crucial role in cellular function. The use of 'deep sequencing' technology (also known as 'next generation sequencing') to infer transcript expression levels in general, and ncRNA specifically, is becoming increasingly common in molecular and clinical laboratories.

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tsmti

Submitted by ChenLiang on Thu, 04/06/2017 - 19:16

Recent studies have revealed that a small non-coding RNA, microRNA (miRNA) down-regulates its mRNA targets. This effect is regarded as an important role in various biological processes. Many studies have been devoted to predicting miRNA-target interactions. These studies indicate that the interactions may only be functional in some specific tissues, which depend on the characteristics of an miRNA. No systematic methods have been established in the literature to investigate the correlation between miRNA-target interactions and tissue specificity through microarray data.

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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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CLIPSeqTools

Submitted by ChenLiang on Thu, 04/06/2017 - 17:39

Immunoprecipitation of RNA binding proteins (RBPs) after in vivo crosslinking, coupled with sequencing of associated RNA footprints (HITS-CLIP, CLIP-seq), is a method of choice for the identification of RNA targets and binding sites for RBPs. Compared with RNA-seq, CLIP-seq analysis is widely diverse and depending on the RBPs that are analyzed, the approaches vary significantly, necessitating the development of flexible and efficient informatics tools.

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MISIS

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

In eukaryotes, diverse small RNA (sRNA) populations including miRNAs, siRNAs and piRNAs regulate gene expression and repress transposons, transgenes and viruses. Functional sRNAs are associated with effector proteins based on their size and nucleotide composition. The sRNA populations are currently analyzed by deep sequencing that generates millions of reads which are then mapped to a reference sequence or database. Here we developed a tool called MISIS to view and analyze sRNA maps of genomic loci and viruses which spawn multiple sRNAs.

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mirSOM

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

MicroRNAs (miRNAs) are small non-coding RNAs that regulate transcriptional processes via binding to the target gene mRNA. In animals, this binding is imperfect, which makes the computational prediction of animal miRNA targets a challenging task. The accuracy of miRNA target prediction can be improved with the use of machine learning methods. Previous work has described methods using supervised learning, but they suffer from the lack of adequate training examples, a common problem in miRNA target identification, which often leads to deficient generalization ability.

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