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A gene (or genetic) regulatory network (GRN) is a collection of molecular regulators that interact with each other and with other substances in the cell to govern the gene expression levels of mRNA and proteins. These play a central role in morphogenesis, the creation of body structures, which in turn is central to evolutionary developmental biology (evo-devo). [Source: Wikipedia]

GraP

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

Cotton (Gossypium spp.) is one of the most important natural fiber and oil crops worldwide. Improvement of fiber yield and quality under changing environments attract much attention from cotton researchers; however, a functional analysis platform integrating omics data is still missing. The success of cotton genome sequencing and large amount of available transcriptome data allows the opportunity to establish a comprehensive analysis platform for integrating these data and related information.

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DisTMGneT

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

It is now widely accepted that microRNAs (miRNAs or miRs) along with transcription factors (TFs) weave a complex inter-regulatory network within the cell that is responsible for the combinatorial regulation of gene expression. Recently we have shown that miRNAs and TFs that form network clusters are also associated with a number of common diseases. However, the quest persists to find out topological structures that facilitate disease progression. In the current work we choose colorectal and breast cancers for our analysis.

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ppt-miRBase

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

miRNAs are non-coding small RNAs that involve diverse biological processes. Until now, little is known about their roles in plant drought resistance. Physcomitrella patens is highly tolerant to drought; however, it is not clear about the basic biology of the traits that contribute P. patens this important character. In this work, we discovered 16 drought stress-associated miRNA (DsAmR) families in P. patens through computational analysis.

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rSNPBase

Submitted by ChenLiang on Thu, 04/06/2017 - 18:58

In recent years, human regulatory SNPs (rSNPs) have been widely studied. Here, we present database rSNPBase, freely available at http://rsnp.psych.ac.cn/, to provide curated rSNPs that analyses the regulatory features of all SNPs in the human genome with reference to experimentally supported regulatory elements. In contrast with previous SNP functional annotation databases, rSNPBase is characterized by several unique features.

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miRTex

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

MicroRNAs (miRNAs) regulate a wide range of cellular and developmental processes through gene expression suppression or mRNA degradation. Experimentally validated miRNA gene targets are often reported in the literature. In this paper, we describe miRTex, a text mining system that extracts miRNA-target relations, as well as miRNA-gene and gene-miRNA regulation relations. The system achieves good precision and recall when evaluated on a literature corpus of 150 abstracts with F-scores close to 0.90 on the three different types of relations.

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A combinatorial approach to determine the context-dependent role in transcriptional and posttranscriptional regulation in Arabidopsis thaliana

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

While progresses have been made in mapping transcriptional regulatory networks, posttranscriptional regulatory roles just begin to be uncovered, which has arrested much attention due to the discovery of miRNAs. Here we demonstrated a combinatorial approach to incorporate transcriptional and posttranscriptional regulatory sequences with gene expression profiles to determine their probabilistic dependencies.

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miRMAP (Visualization)

Submitted by ChenLiang on Sun, 01/08/2017 - 16:16

MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression at a post-transcriptional level. An miRNA may target many messenger RNA (mRNA) transcripts, and each transcript may be targeted by multiple miRNAs. Our understanding of miRNA regulation is evolving to consider modules of miRNAs that regulate groups of functionally related mRNAs. Here we expand the model of miRNA functional modules and use it to guide the integration of miRNA and mRNA expression and target prediction data.

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tasiRNAdb

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

In plants, many trans-acting small interfering RNA (ta-siRNA) regulatory pathways have been identified as significant components of the gene networks involved in development, metabolism, responses to biotic and abiotic stresses and DNA methylation at the TAS locus.

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cGRNB

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

We are witnessing rapid progress in the development of methodologies for building the combinatorial gene regulatory networks involving both TFs (Transcription Factors) and miRNAs (microRNAs). There are a few tools available to do these jobs but most of them are not easy to use and not accessible online. A web server is especially needed in order to allow users to upload experimental expression datasets and build combinatorial regulatory networks corresponding to their particular contexts.

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SmiRN-AD

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

Alzheimer's disease (AD) is an incurable neurodegenerative disorder. Much effort has been devoted to developing effective therapeutic agents. Recently, targeting microRNAs (miRNAs) with small molecules has become a novel therapy for human diseases. In this study, we present a systematic computational approach to construct a bioactive Small molecule and miRNA association Network in AD (SmiRN-AD), which is based on the gene expression signatures of bioactive small molecule perturbation and AD-related miRNA regulation.

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