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Transcription factor interaction detection software tools | Genome annotation

Here, we surveyed bioinformatics software tools for predicting cooperative transcription factor. Transcriptional regulation of gene expression is one of the major mechanisms for cells to respond to environmental and physiological changes. This…
Computational…
Algorithm

Computational identification of cooperative transcription factor pairs

Four simple algorithms, which aim to investigate whether the performance of…

Four simple algorithms, which aim to investigate whether the performance of computational identification of cooperative TF pairs could be improved by using a more biologically relevant way to define…

Motif-PIE
Desktop

Motif-PIE

An approach to understand interactions between TFs. Motif-PIE has been tested…

An approach to understand interactions between TFs. Motif-PIE has been tested using Saccharomyces cerevisiae as a model system. Instead of gene expression profiles, we focus on the sequence motifs in…

simTFBS
Algorithm

simTFBS

A method that incorporates de novo motif discovery in the procedures of…

A method that incorporates de novo motif discovery in the procedures of analyzing ChIP-chip data. simTFBS employs the discovered motifs to refine the lists of target genes, which further improve the…

Identification…
Desktop

Identification of transcription factor cooperativity via stochastic system model

A measurement of transcription factor cooperativity developed according to the…

A measurement of transcription factor cooperativity developed according to the regulatory abilities of cooperative transcription factor pairs and the number of their occurrences. Transcription factor…

AdaFuzzy
Algorithm

AdaFuzzy

A further enhanced machine-learning (adaptive fuzzy) approach, to infer…

A further enhanced machine-learning (adaptive fuzzy) approach, to infer transcriptional interactions (Tis), which incorporates DNA sequence, ChIP-chip and microarray data. AdaFuzzy proposes a robust…

MOFA
Algorithm

MOFA MOdule Finding Algorithm

An algorithm developed to reconstruct transcriptional regulatory modules (TRMs)…

An algorithm developed to reconstruct transcriptional regulatory modules (TRMs) of the yeast cell cycle by integrating gene expression data and ChIP-chip data. MOFA identified 87 TRMs, which together…

CoopTFD
Dataset

CoopTFD Cooperative Transcription Factors Database

A repository for 2622 yeast cooperative transcription factors pairs predicted…

A repository for 2622 yeast cooperative transcription factors pairs predicted by 17 existing algorithms. CoopTFD provides five types of validation information to help users judge the biological…

PCTFPeval
Web

PCTFPeval Predicted Cooperative TF Pair evaluator

A web tool for benchmarking newly developed algorithms for predicting…

A web tool for benchmarking newly developed algorithms for predicting cooperative transcription factor pairs in yeast. PCTFPeval allows users to input a list of predicted cooperative TF pairs from…

TFcooperativity
Algorithm

TFcooperativity

An expectation maximization algorithm to use log-linear models to infer whether…

An expectation maximization algorithm to use log-linear models to infer whether two transcription factors participate in co-operative gene regulation. Simulation studies show that our proposed…

LICORN
Algorithm

LICORN Learning co-operative regulation networks

A data mining system for inferring transcriptional regulation relationships…

A data mining system for inferring transcriptional regulation relationships from RNA expression values. LICORN is particularly suitable for the detection of cooperative transcriptional regulation. We…

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