Expresso: A database and web server for exploring the interaction of transcription factors and their target genes in Arabidopsis thaliana using ChIP-Seq peak data
| Autor: | Lenwood S. Heath, Karthik Raja Velmurugan, Ruth Grene, Doaa Altarawy, Delasa Aghamirzaie, Shuchi Wu |
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| Jazyk: | angličtina |
| Rok vydání: | 2017 |
| Předmět: |
0106 biological sciences
0301 basic medicine Web server Relational database Bioinformatics Biology computer.software_genre 01 natural sciences General Biochemistry Genetics and Molecular Biology 03 medical and health sciences ChIP-Seq Arabidopsis Gene expression Transcriptional regulation natural sciences transcriptional regulation General Pharmacology Toxicology and Pharmaceutics Gene Transcription factor transcription factor Regulation of gene expression General Immunology and Microbiology Database Software Tool Article General Medicine Articles Genomics biology.organism_classification 030104 developmental biology Plant Genetics & Gene Expression gene regulation computer 010606 plant biology & botany |
| Zdroj: | F1000Research |
| ISSN: | 2046-1402 |
| Popis: | Motivation: The increasing availability of chromatin immunoprecipitation sequencing (ChIP-Seq) data enables us to learn more about the action of transcription factors in the regulation of gene expression. Even though in vivo transcriptional regulation often involves the concerted action of more than one transcription factor, the format of each individual ChIP-Seq dataset usually represents the action of a single transcription factor. Therefore, a relational database in which available ChIP-Seq datasets are curated is essential. Results: We present Expresso (database and webserver) as a tool for the collection and integration of available Arabidopsis ChIP-Seq peak data, which in turn can be linked to a user’s gene expression data. Known target genes of transcription factors were identified by motif analysis of publicly available GEO ChIP-Seq data sets. Expresso currently provides three services: 1) Identification of target genes of a given transcription factor; 2) Identification of transcription factors that regulate a gene of interest; 3) Computation of correlation between the gene expression of transcription factors and their target genes. Availability: Expresso is freely available at http://bioinformatics.cs.vt.edu/expresso/ |
| Databáze: | OpenAIRE |
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