ApicoTFdb: the comprehensive web repository of apicomplexan transcription factors and transcription-associated co-factors.

Apicomplexa / classification Databases, Protein Internet Protozoan Proteins / genetics Transcription Factors / genetics

Journal

Database : the journal of biological databases and curation
ISSN: 1758-0463
Titre abrégé: Database (Oxford)
Pays: England
ID NLM: 101517697

Informations de publication

Date de publication:
01 01 2019
Historique:
received: 05 03 2019
revised: 28 04 2019
accepted: 28 06 2019
entrez: 19 9 2019
pubmed: 19 9 2019
medline: 7 2 2020
Statut: ppublish

Résumé

Despite significant progress in apicomplexan genome sequencing and genomics, the current list of experimentally validated transcription factors (TFs) in these genomes is incomplete and mainly consists of AP2 family of proteins, with only a limited number of non-AP2 family TFs and transcription-associated co-factors (TcoFs). We have performed a systematic bioinformatics-aided prediction of TFs and TcoFs in apicomplexan genomes and developed the ApicoTFdb database which consists of experimentally validated as well as computationally predicted TFs and TcoFs in 14 apicomplexan species. The predicted TFs are manually curated to complement the existing annotations. The current version of the database includes 1292 TFs which includes experimentally validated and computationally predicted TFs, representing 20 distinct families across 14 apicomplexan species. The predictions include TFs of TUB, NAC, BSD, HTH, Cupin/Jumonji, winged helix and FHA family proteins, not reported earlier as TFs in the genomes. Apart from TFs, ApicoTFdb also classifies TcoFs into three main subclasses: TRs, CRRs and RNARs, representing 2491 TcoFs in 14 apicomplexan species, are analyzed in this study. The database is designed to integrate different tools for comparative analysis. All entries in the database are dynamically linked with other databases, literature reference, protein-protein interactions, pathways and annotations associated with each protein. ApicoTFdb will be useful to the researchers interested in less-studied gene regulatory mechanisms mediating the complex life cycle of the apicomplexan parasites. The database will aid in the discovery of novel drug targets to much needed combat the growing drug resistance in the parasites.

Identifiants

DOI: 10.1093/database/baz094 PMID: 31529106 PMC: PMC6748703
pubmed: 31529106
pii: 5560306
doi: 10.1093/database/baz094
pmc: PMC6748703
pii:
doi:

Substances chimiques

Protozoan Proteins 0
Transcription Factors 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Informations de copyright

© The Author(s) 2019. Published by Oxford University Press.

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Auteurs

Rahila Sardar (R)

Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.
Department of Biochemistry, Jamia Hamdard, Hamdard Nagar, New Delhi 110057, India.

Abhinav Kaushik (A)

Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.

Rajan Pandey (R)

Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.

Asif Mohmmed (A)

Parasite Cell Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.

Shakir Ali (S)

Department of Biochemistry, Jamia Hamdard, Hamdard Nagar, New Delhi 110057, India.

Dinesh Gupta (D)

Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Alveolata › Apicomplexa › ApicoTFdb: the comprehensive web repository of...
questionsmedicales.fr › Sciences de l'information › Mémorisation et recherche des informations › Bases de données comme sujet › Bases de données factuelles › Bases de données génétiques › Bases de données de protéines › ApicoTFdb: the comprehensive web repository of...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Systèmes informatiques › Réseaux de communication entre ordinateurs › Internet › ApicoTFdb: the comprehensive web repository of...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines de protozoaire › ApicoTFdb: the comprehensive web repository of...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Facteurs de transcription › ApicoTFdb: the comprehensive web repository of...