YPA

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YPA

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:02.926258

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ypa

metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:02.926258

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Other names: ypa

YPA (Yeast Promoter Atlas) is a repository of promoter features in Saccharomyces cerevisiae. It intergrates various resources (including promoter sequences, TSSs, TATA boxes, TFBSs, nucleosome occupancy, DNA bendability, TF-TF interaction, and gene expression data) and provides a comprehensive view of the promoter regions.

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Publications:

Publications

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YPA: an integrated repository of promoter features in Saccharomyces cerevisiae
PMID: 21045055

metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:02.926258

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http://nar.oxfordjournals.org/content/39/suppl_1/D647

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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• YPA: an integrated repository of promoter features in Saccharomyces cerevisiae PubMed citations: 23.

  23 articles citing: YPA: an integrated repository of promoter features in Saccharomyces cerevisiae

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  Promoter tools for further development of Aspergillus oryzae as a platform for fungal secondary metabolite production. PMID:32211196

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  Regulation of Skn7-dependent, oxidative stress-induced genes by the RNA polymerase II-CTD phosphatase, Fcp1, and Mediator kinase subunit, Cdk8, in yeast. PMID:31506296

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  YGMD: a repository for yeast cooperative transcription factor sets and their target gene modules. PMID:29220473

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  YEASTRACT: an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae. PMID:29036684

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  Abf1 and other general regulatory factors control ribosome biogenesis gene expression in budding yeast. PMID:28158860

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  Saccharomyces cerevisiae single-copy plasmids for auxotrophy compensation, multiple marker selection, and for designing metabolically cooperating communities. PMID:27830062

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  Identification of key player genes in gene regulatory networks. PMID:27599550

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  Ndt80 activates the meiotic ORC1 transcript isoform and SMA2 via a bi-directional middle sporulation element in Saccharomyces cerevisiae. PMID:27362276

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  Multiple roles of the general regulatory factor Abf1 in yeast ribosome biogenesis. PMID:27262581

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  YAGM: a web tool for mining associated genes in yeast based on diverse biological associations. PMID:26678566

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  PCTFPeval: a web tool for benchmarking newly developed algorithms for predicting cooperative transcription factor pairs in yeast. PMID:26677932

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  A regulatory similarity measure using the location information of transcription factor binding sites in Saccharomyces cerevisiae. PMID:25560196

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  SPoRE: a mathematical model to predict double strand breaks and axis protein sites in meiosis. PMID:25495332

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  Identifying transcription factor complexes and their roles. PMID:25161228

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  Design of synthetic yeast promoters via tuning of nucleosome architecture. PMID:24862902

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  Identifying functional transcription factor binding sites in yeast by considering their positional preference in the promoters. PMID:24386279

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  The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. PMID:24170807

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  High-throughput genetic and gene expression analysis of the RNAPII-CTD reveals unexpected connections to SRB10/CDK8. PMID:24009531

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  Use of expression-enhancing terminators in Saccharomyces cerevisiae to increase mRNA half-life and improve gene expression control for metabolic engineering applications. PMID:23856240

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  Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data. PMID:22898448

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  Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report. PMID:22434826

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  A study on promoter characteristics of head-to-head genes in Saccharomyces cerevisiae. PMID:22369481

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  YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities. PMID:22102575
• http://nar.oxfordjournals.org/content/39/suppl_1/D647

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genomics databases (non-vertebrate)

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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fungal genome databases

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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transcription factors and regulatory sites

metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:02.926258

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gene expression

metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:02.926258

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dna binding sites

metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:02.926258

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gene transcripts

metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:02.926258

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model organisms

metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:02.926258

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genomics fungal genome transcription factors and regulatory sites gene expression dna binding sites gene transcripts model organisms