YCRD: Yeast Combinatorial Regulation Database

Wu, Wei; Hsieh, Yen Chen; Lai, Fu Jou

doi:10.1371/journal.pone.0159213

Cited by 2 publications

(3 citation statements)

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“…Many algorithms have been proposed to identify cooperative TF pairs in yeast [ 4 – 20 ]. Different algorithms are developed based on different rationales and their performances vary under different evaluation criteria [ 21 – 24 ]. For example, two algorithms [ 4 , 6 ] assume that the genes bound by both TFs of a cooperative TF pair are more co-expressed or closer in the protein-protein interaction network than are genes bound by either TF alone.…”

Section: Introductionmentioning

confidence: 99%

Detecting Cooperativity between Transcription Factors Based on Functional Coherence and Similarity of Their Target Gene Sets

Lai

2016

PLoS ONE

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In eukaryotic cells, transcriptional regulation of gene expression is usually achieved by cooperative transcription factors (TFs). Therefore, knowing cooperative TFs is the first step toward uncovering the molecular mechanisms of gene expression regulation. Many algorithms based on different rationales have been proposed to predict cooperative TF pairs in yeast. Although various types of rationales have been used in the existing algorithms, functional coherence is not yet used. This prompts us to develop a new algorithm based on functional coherence and similarity of the target gene sets to identify cooperative TF pairs in yeast. The proposed algorithm predicted 40 cooperative TF pairs. Among them, three (Pdc2-Thi2, Hot1-Msn1 and Leu3-Met28) are novel predictions, which have not been predicted by any existing algorithms. Strikingly, two (Pdc2-Thi2 and Hot1-Msn1) of the three novel predictions have been experimentally validated, demonstrating the power of the proposed algorithm. Moreover, we show that the predictions of the proposed algorithm are more biologically meaningful than the predictions of 17 existing algorithms under four evaluation indices. In summary, our study suggests that new algorithms based on novel rationales are worthy of developing for detecting previously unidentifiable cooperative TF pairs.

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Section: Introductionmentioning

confidence: 99%

Detecting Cooperativity between Transcription Factors Based on Functional Coherence and Similarity of Their Target Gene Sets

Lai

2016

PLoS ONE

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“…Second, Cooperative Transcription Factors Database (CoopTFD) ( 25 ) has a comprehensive collection of 2622 predicted cooperative TF pairs in yeast from 17 existing algorithms. Third, Yeast Combinatorial Regulation Database (YCRD) ( 17 ) deposits 434197 regulatory associations between 2535 cooperative TF pairs and 6243 genes. In this study, we present YGMD to provide 34 120 CoopTFSs, each of which consists of two to five cooperative TFs, and their target GMs.…”

Section: Utility and Discussionmentioning

confidence: 99%

“…The regulatory associations between a TF and its target GM are supported by experimental evidence in the literature. Second, YCRD ( 17 ) collects 2535 GMs, each of which is regulated by a predicted cooperative TF pair. The regulatory associations between a predicted cooperative TF pair and its target GM are supported by experimental evidence in the literature.…”

Section: Introductionmentioning

confidence: 99%

YGMD: a repository for yeast cooperative transcription factor sets and their target gene modules

Chen

et al. 2017

Database

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By organizing the genome into gene modules (GMs), a living cell coordinates the activities of a set of genes to properly respond to environmental changes. The transcriptional regulation of the expression of a GM is usually carried out by a cooperative transcription factor set (CoopTFS) consisting of several cooperative transcription factors (TFs). Therefore, a database which provides CoopTFSs and their target GMs is useful for studying the cellular responses to internal or external stimuli. To address this need, here we constructed YGMD (Yeast Gene Module Database) to provide 34120 CoopTFSs, each of which consists of two to five cooperative TFs, and their target GMs. The cooperativity between TFs in a CoopTFS is suggested by physical/genetic interaction evidence or/and predicted by existing algorithms. The target GM regulated by a CoopTFS is defined as the common target genes of all the TFs in that CoopTFS. The regulatory association between any TF in a CoopTFS and any gene in the target GM is supported by experimental evidence in the literature. In YGMD, users can (i) search the GM regulated by a specific CoopTFS of interest or (ii) search all possible CoopTFSs whose target GMs contain a specific gene of interest. The biological relevance of YGMD is shown by a case study which demonstrates that YGMD can provide a GM enriched with genes known to be regulated by the query CoopTFS (Cbf1-Met4-Met32). We believe that YGMD provides a valuable resource for yeast biologists to study the transcriptional regulation of GMs. Database URL: http://cosbi4.ee.ncku.edu.tw/YGMD/, http://cosbi5.ee.ncku.edu.tw/YGMD/ or http://cosbi.ee.ncku.edu.tw/YGMD/

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YCRD: Yeast Combinatorial Regulation Database

Cited by 2 publications

References 35 publications

Detecting Cooperativity between Transcription Factors Based on Functional Coherence and Similarity of Their Target Gene Sets

Detecting Cooperativity between Transcription Factors Based on Functional Coherence and Similarity of Their Target Gene Sets

YGMD: a repository for yeast cooperative transcription factor sets and their target gene modules

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