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Transcription Factors (TFs)

TFmiR

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

TFmiR is a freely available web server for deep and integrative analysis of combinatorial regulatory interactions between transcription factors, microRNAs and target genes that are involved in disease pathogenesis. Since the inner workings of cells rely on the correct functioning of an enormously complex system of activating and repressing interactions that can be perturbed in many ways, TFmiR helps to better elucidate cellular mechanisms at the molecular level from a network perspective.

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BRB-ArrayTools

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

A Gene Set Expression Comparison kit is developed as a module of BRB-ArrayTools for discovering biologically meaningful patterns in gene expression data. The kit consists of gene sets of transcription factor (TF) targets, gene sets containing genes whose protein products share the same protein domain and gene sets of microRNA targets. Using this module of BRB-ArrayTools, researchers can efficiently analyze pre-defined sets of gene whose expression is correlated with a categorical quantitative phenotype or patient survival.

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PuTmiR

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

Some of the recent investigations in systems biology have revealed the existence of a complex regulatory network between genes, microRNAs (miRNAs) and transcription factors (TFs). In this paper, we focus on TF to miRNA regulation and provide a novel interface for extracting the list of putative TFs for human miRNAs. A putative TF of an miRNA is considered here as those binding within the close genomic locality of that miRNA with respect to its starting or ending base pair on the chromosome.

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CRSD

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

Transcription factors (TFs) and microRNAs play important roles in the regulation of human gene expression, and the study of their combinatory regulations of gene expression is a new research field. We constructed a comprehensive web server, the composite regulatory signature database (CRSD), that can be applied in investigating complex regulatory behaviors involving gene expression signatures (GESs), microRNA regulatory signatures (MRSs) and TF regulatory signatures (TRSs).

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TMREC

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

Over the past decades, studies have reported that the combinatorial regulation of transcription factors (TFs) and microRNAs (miRNAs) is essential for the appropriate execution of biological events and developmental processes. Dysregulations of these regulators often cause diseases. However, there are no available resources on the regulatory cascades of TFs and miRNAs in the context of human diseases. To fulfill this vacancy, we established the TMREC database in this study.

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AthaMap

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

The AthaMap database generates a map of predicted transcription factor binding sites (TFBS) for the whole Arabidopsis thaliana genome. AthaMap has now been extended to include data on post-transcriptional regulation. A total of 403,173 genomic positions of small RNAs have been mapped in the A. thaliana genome. These identify 5772 putative post-transcriptionally regulated target genes.

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PmmR

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

To date, a significant amount of research has been conducted for computational modeling of the microRNA (miRNA)-target gene interactions and inferring different kinds of biologically relevant association from their variable expressions, available from microarray experiments. However, topological organization of the miRNA-transcription factor (TF) induced regulatory network has not yet been analyzed at a genome scale. Evidently, by ignoring the regulatory relationship among the constituent molecules, we expose our model to a great deal of noise.

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FANTOM4 EdgeExpressDB

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

EdgeExpressDB is a novel database and set of interfaces for interpreting biological networks and comparing large high-throughput expression datasets that requires minimal development for new data types and search patterns. The FANTOM4 EdgeExpress database http://fantom.gsc.riken.jp/4/edgeexpress summarizes gene expression patterns in the context of alternative promoter structures and regulatory transcription factors and microRNAs using intuitive gene-centric and sub-network views.

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miRegulome

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

miRNAs regulate post transcriptional gene expression by targeting multiple mRNAs and hence can modulate multiple signalling pathways, biological processes, and patho-physiologies. Therefore, understanding of miRNA regulatory networks is essential in order to modulate the functions of a miRNA. The focus of several existing databases is to provide information on specific aspects of miRNA regulation. However, an integrated resource on the miRNA regulome is currently not available to facilitate the exploration and understanding of miRNA regulomics.

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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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