Analysis of stress related sequences in plant genomes
KrishiKosh
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Title |
Analysis of stress related sequences in plant genomes
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Creator |
B. N, Mahantesha Naika
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Contributor |
R, Sowdhamini
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Subject |
genes, planting, transcription, proteins, transcription factors, communication technology, enzymes, acidity, genomes, biological phenomena
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Description |
Understanding the principles of abiotic and biotic stress response mechanisms and application of knowledge derived from integrated experimental and bioinformatics approaches are gaining importance in agriculture. The study employed an integrated biocuration and genomic data mining approach to characterize the dataset of transcription factors and consensus binding sites from literature mining and stress responsive genes from expression studies. Study used an in-house developed STIF algorithm for predicting the transcription factor binding sites in stress responsive genes. In addition to the extensive content present in the first version, STIFDB2 had now been updated with 15 stress signals, 31 transcription factors and 5984 stress-responsive genes from three species (Arabidopsis thaliana, Oryza sativa L. ssp. japonica and Oryza sativa L. ssp. indica) and also contain orthologs from other agricultural important crop plants. STIFDB2 database is available at the URL http://caps.ncbs.res.in/stifdb2. STIFDB2 also reports the stressresponsive genes data analyzed using enrichment-based meta-analysis framework consisting of Gene and Plant Ontology, biological pathway and functional domain annotations in Arabidopsis thaliana. Study found several ontologies, shared and unique ones, pathways, domains and phenotypic characters associated with stress responsive genes. In the protein-protein interaction network mediated by stress responsive genes, study found the 26S proteasome subunits as a highly clustered module using molecular complex detection algorithm and, Enrichment analysis indicates that several biological processes including ‘flower development’ are associated with the network. Study performed homology modelling and docking studies of corresponding protein products of the stress responsive genes to gain better insights into their structure and function. Results from these studies can be used to develop better varieties of crop plants. |
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Date |
2016-05-21T09:08:51Z
2016-05-21T09:08:51Z 2013-09-16 |
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Type |
Thesis
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Identifier |
Th-10642
http://krishikosh.egranth.ac.in/handle/1/66185 |
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Language |
en
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Format |
application/pdf
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Publisher |
University of Agricultural Sciences, Bengaluru
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