Phylogeny, Functional Annotation, and Protein Interaction Network Analyses of the Xenopus tropicalis Basic Helix-Loop-Helix Transcription Factors
Joint Authors
Source
Issue
Vol. 2013, Issue 2013 (31 Dec. 2013), pp.1-15, 15 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2013-11-10
Country of Publication
Egypt
No. of Pages
15
Main Subjects
Abstract EN
The previous survey identified 70 basic helix-loop-helix (bHLH) proteins, but it was proved to be incomplete, and the functional information and regulatory networks of frog bHLH transcription factors were not fully known.
Therefore, we conducted an updated genome-wide survey in the Xenopus tropicalis genome project databases and identified 105 bHLH sequences.
Among the retrieved 105 sequences, phylogenetic analyses revealed that 103 bHLH proteins belonged to 43 families or subfamilies with 46, 26, 11, 3, 15, and 4 members in the corresponding supergroups.
Next, gene ontology (GO) enrichment analyses showed 65 significant GO annotations of biological processes and molecular functions and KEGG pathways counted in frequency.
To explore the functional pathways, regulatory gene networks, and/or related gene groups coding for Xenopus tropicalis bHLH proteins, the identified bHLH genes were put into the databases KOBAS and STRING to get the signaling information of pathways and protein interaction networks according to available public databases and known protein interactions.
From the genome annotation and pathway analysis using KOBAS, we identified 16 pathways in the Xenopus tropicalis genome.
From the STRING interaction analysis, 68 hub proteins were identified, and many hub proteins created a tight network or a functional module within the protein families.
American Psychological Association (APA)
Liu, Wu-yi& Chen, Deyu. 2013. Phylogeny, Functional Annotation, and Protein Interaction Network Analyses of the Xenopus tropicalis Basic Helix-Loop-Helix Transcription Factors. BioMed Research International،Vol. 2013, no. 2013, pp.1-15.
https://search.emarefa.net/detail/BIM-1030112
Modern Language Association (MLA)
Liu, Wu-yi& Chen, Deyu. Phylogeny, Functional Annotation, and Protein Interaction Network Analyses of the Xenopus tropicalis Basic Helix-Loop-Helix Transcription Factors. BioMed Research International No. 2013 (2013), pp.1-15.
https://search.emarefa.net/detail/BIM-1030112
American Medical Association (AMA)
Liu, Wu-yi& Chen, Deyu. Phylogeny, Functional Annotation, and Protein Interaction Network Analyses of the Xenopus tropicalis Basic Helix-Loop-Helix Transcription Factors. BioMed Research International. 2013. Vol. 2013, no. 2013, pp.1-15.
https://search.emarefa.net/detail/BIM-1030112
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1030112