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PLoS One. 2013 Jun 18;8(6):e66521. doi: 10.1371/journal.pone.0066521. Print 2013.

Dissecting the Characteristics and Dynamics of Human Protein Complexes at Transcriptome Cascade Using RNA-Seq Data.

Author information

1
The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.

Abstract

Human protein complexes play crucial roles in various biological processes as the functional module. However, the expression features of human protein complexes at the transcriptome cascade are poorly understood. Here, we used the RNA-Seq data from 16 disparate tissues and four types of human cancers to explore the characteristics and dynamics of human protein complexes. We observed that many individual components of human protein complexes can be generated by multiple distinct transcripts. Similar with yeast, the human protein complex constituents are inclined to co-express in diverse tissues. The dominant isoform of the genes involved in protein complexes tend to encode the complex constituents in each tissue. Our results indicate that the protein complex dynamics not only correlate with the presence or absence of complexes, but may also be related to the major isoform switching for complex subunits. Between any two cancers of breast, colon, lung and prostate, we found that only a few of the differentially expressed transcripts associated with complexes were identical, but 5-10 times more protein complexes involved in differentially expressed transcripts were common. Collectively, our study reveals novel properties and dynamics of human protein complexes at the transcriptome cascade in diverse normal tissues and different cancers.

PMID:
23824284
PMCID:
PMC3688907
DOI:
10.1371/journal.pone.0066521
[Indexed for MEDLINE]
Free PMC Article

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