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Identification of salt treated proteins in sorghum using gene ontology linkage.

ABSTRACT: Sorghum bicolor (L.) is an important crop of arid and semi arid zones with most of its varieties tolerant to drought, heat and salt stress. Functional identification of many salt tolerant proteins has been reported in Arabidopsis, rice and other plants, however only little functional information has been predicted in sorghum till date. A 2-D gel electrophoresis based proteomic approach with MALDI-TOF mass spectrometer was utilized to analyze the salt stress response of sorghum. Major changes in protein complement were observed at 200 mM NaCl in hydroponic culture after 96 h of salt-stress. Highly expressed five proteins were excised for functional identification. We developed shortest path (SP) analysis based method on Gene Ontology (GO) hierarchy using sum of GO-term's semantic similarities. In this study, we observed that majority of expressed proteins belonged to the functional category of energy production and conversion, signal transduction mechanisms and ribosome maturation. These identified functions suggest a distinct mechanism of salt-stress adaptation in sorghum plant. The proposed method in this paper potentially has great importance to further understanding of newly identified proteins that can help in plant development.

SUBMITTER: Sekhwal MK

PROVIDER: S-EPMC3550515 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature

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Identification of salt treated proteins in sorghum using gene ontology linkage.

Sekhwal Manoj Kumar MK Swami Ajit Kumar AK Sarin Renu R Sharma Vinay V

Physiology and molecular biology of plants : an international journal of functional plant biology 20120701 3

Sorghum bicolor (L.) is an important crop of arid and semi arid zones with most of its varieties tolerant to drought, heat and salt stress. Functional identification of many salt tolerant proteins has been reported in Arabidopsis, rice and other plants, however only little functional information has been predicted in sorghum till date. A 2-D gel electrophoresis based proteomic approach with MALDI-TOF mass spectrometer was utilized to analyze the salt stress response of sorghum. Major changes in ...[more]

PMID: 23814435

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Project description:BackgroundFever is one of the most common adverse events of vaccines. The detailed mechanisms of fever and vaccine-associated gene interaction networks are not fully understood. In the present study, we employed a genome-wide, Centrality and Ontology-based Network Discovery using Literature data (CONDL) approach to analyse the genes and gene interaction networks associated with fever or vaccine-related fever responses.ResultsOver 170,000 fever-related articles from PubMed abstracts and titles were retrieved and analysed at the sentence level using natural language processing techniques to identify genes and vaccines (including 186 Vaccine Ontology terms) as well as their interactions. This resulted in a generic fever network consisting of 403 genes and 577 gene interactions. A vaccine-specific fever sub-network consisting of 29 genes and 28 gene interactions was extracted from articles that are related to both fever and vaccines. In addition, gene-vaccine interactions were identified. Vaccines (including 4 specific vaccine names) were found to directly interact with 26 genes. Gene set enrichment analysis was performed using the genes in the generated interaction networks. Moreover, the genes in these networks were prioritized using network centrality metrics. Making scientific discoveries and generating new hypotheses were possible by using network centrality and gene set enrichment analyses. For example, our study found that the genes in the generic fever network were more enriched in cell death and responses to wounding, and the vaccine sub-network had more gene enrichment in leukocyte activation and phosphorylation regulation. The most central genes in the vaccine-specific fever network are predicted to be highly relevant to vaccine-induced fever, whereas genes that are central only in the generic fever network are likely to be highly relevant to generic fever responses. Interestingly, no Toll-like receptors (TLRs) were found in the gene-vaccine interaction network. Since multiple TLRs were found in the generic fever network, it is reasonable to hypothesize that vaccine-TLR interactions may play an important role in inducing fever response, which deserves a further investigation.ConclusionsThis study demonstrated that ontology-based literature mining is a powerful method for analyzing gene interaction networks and generating new scientific hypotheses.

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Identification of salt treated proteins in sorghum using gene ontology linkage.

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Identification of salt treated proteins in sorghum using gene ontology linkage.

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