In silico analysis of transcription factor repertoires and prediction of stress-responsive transcription factors from six major Gramineae plants. DNA Res 2011;... K Mochida,T Yoshida,T Sakurai,... - 《Dna Research》 被引量: 203发表: 2009年 Editor's Choice: In Silico Analysis of Transcription ...
Transfind transcription factor prediction.Seth, B. GarrenYuvabharath, KondaveetiMichael, O. DuffGordon, G. Carmichael
DeepTFactor predicted 332 candidate TFs in Escherichia coli K-12 MG1655. Among them, 84 candidate TFs belong to the y-ome, which is a collection of genes that lack experimental evidence of function. We experimentally validated the results of DeepTFactor prediction by further characterizing genome...
Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal - GitHub - loosolab/TOBIAS: Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
biological process of cell cycle is over-represented at most distance constraints tested. In the case of NFAT, major over-represented biological functions include homophilic cell adhesion and immune response. As mentioned above, immune response is directly controlled by NFAT transcription factor. Overall...
Such prediction models were constructed based on the compilation of known promoter sequences for each sigma factor. In E.coli, RegulonDB (5) contains both experimental and predicted cis- elements and is suited to the above-mentioned analyses while there are no databases containing comprehensive ...
Mathelier A and Wasserman WW: The next generation of transcription factor binding site prediction. PLoS Comput Biol. 9(e1003214)2013.PubMed/NCBIView Article:Google Scholar 23 Schneider TD and Stephens RM: Sequence logos: A new way to display consensus sequences. Nucleic Acids Res. 18:6097–...
Kummerfeld SK, Teichmann SA: DBD: a transcription factor prediction database. Nucleic Acids Res. 2006, 34: D74-D81. 10.1093/nar/gkj131. Article PubMed CAS PubMed Central Google Scholar BDGP gene expression patterns resource. [http://insitu.fruitfly.org] Adryan B, Teichmann SA: The dev...
syringae TFs were compiled based on annotations in the DBD: Transcription-factor prediction database (www.transcriptionfactor.org)22, altogether resulting in 301 TFs included in the present study (Fig. 1a). Almost all analyzed TFs contained the DNA-binding domains (DBDs) of helix–turn–helix ...
Recently, deep learning based models have been proposed and have shown competitive results on a transcription factor binding site prediction task. However, it is difficult to interpret the prediction results obtained from the previous models. In addition, the previous models assumed all the sequence ...