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Genome-wide identification, classification and functional analyses of the bHLH transcription factor family in the pig, Sus scrofa

Molecular Genetics and Genomics volume 290, pages 1415–1433 (2015)Cite this article

Abstract

The basic helix–loop–helix (bHLH) transcription factors are one of the largest families of gene regulatory proteins and play crucial roles in genetic, developmental and physiological processes in eukaryotes. Here, we conducted a survey of the Sus scrofa genome and identified 109 putative bHLH transcription factor members belonging to super-groups A, B, C, D, E, and F, respectively, while four members were orphan genes. We identified 6 most significantly enriched KEGG pathways and 116 most significant GO annotation categories. Further comprehensive surveys in human genome and other 12 medical databases identified 72 significantly enriched biological pathways with these 113 pig bHLH transcription factors. From the functional protein association network analysis 93 hub proteins were identified and 55 hub proteins created a tight network or a functional module within their protein families. Especially, there were 20 hub proteins found highly connected in the functional interaction network. The present study deepens our understanding and provided insights into the evolution and functional aspects of animal bHLH proteins and should serve as a solid foundation for further for analyses of specific bHLH transcription factors in the pig and other mammals.

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Abbreviations

bHLH:

Basic helix–loop–helix

SsbHL:

bHLH in the pig, Sus scrofa

Hs:

Homo sapiens

Ss:

Sus scrofa

PAS:

Per–Arnt–Sim homology

ML:

Maximum likelihood

NJ:

Neighbor joining

MP:

Maximum parsimony

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Acknowledgments

We are grateful to the anonymous reviewers for their suggestions. This work is supported by Anhui Provincial Major Project of Discipline Construction and the 2014 annual Anhui Provincial Project of Outstanding Young Talents Fund in Colleges and Universities. It is also supported by Anhui Provincial Natural Science Foundations (No.1308085QC63, No.1408085QC65) and Anhui Provincial Educational Commission Natural Science Foundations (No. KJ2012A216, KJ2011A210).

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Authors and Affiliations

  1. Department of Biology Sciences, Fuyang Normal College, No.100 West Qing He Road, Fuyang, 236037, People’s Republic of China

    Wuyi Liu

  2. Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province, Fuyang Normal College, Fuyang, 236037, People’s Republic of China

    Wuyi Liu

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Correspondence to Wuyi Liu.

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Communicated by S. Hohmann.

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Liu, W. Genome-wide identification, classification and functional analyses of the bHLH transcription factor family in the pig, Sus scrofa . Mol Genet Genomics 290, 1415–1433 (2015). https://doi.org/10.1007/s00438-015-1007-9

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  • DOI: https://doi.org/10.1007/s00438-015-1007-9

Keywords

  • BHLH transcription factor
  • Sus scrofa BLAST search
  • Phylogenetic analysis
  • Classification
  • Gene ontology
  • Pathway
  • Protein interaction network