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STIFDB2


NAR Molecular Biology Database Collection entry number 1582
Mahantesha Naika1,2, Khader Shameer2,3, Oommen K. Mathew2, Ramanjini Gowda1 and R. Sowdhamini 2*
1Department of Plant Biotechnology, University of Agricultural Sciences, GKVK Campus, Bellary Road, Bangalore 560 065, INDIA 2 National Centre for Biological Sciences (TIFR), UAS-GKVK Campus, Bellary Road, Bangalore 560 065, INDIA 3 Division of Biomedical Statistics and Informatics & Division of Cardiovascular Diseases, Mayo Clinic, Rochester 55905, USA

Database Description

Various genes get upregulated in plants during adverse environmental conditions, which alter the metabolic functions to mitigate the stress effects for adaptation. Therefore, it is important to know the regulatory motifs of stress-induced genes for given stress tolerance. We reported a database of abiotic stress-responsive genes curated from publicly available microarray datasets earlier (1) and HMM-based models were used to identify binding sites for the transcription factors belonging to these stress-inducible genes (2).

Recent Developments

We now provide update with additional genes, transcription factors, species, and stress signals. We have also integrated more comprehensive information for abiotic stress responsive genes and their transcription factor binding sites. We refer to this update as STIFDB2 (Stress Responsive Transcription Factor Database version 2). During the update involving 3355 stress-responsive genes, several inclusions were made: like the addition of few more transcription factors, one agriculturally important model plant Oryza sativa and additional abiotic stresses (like heat, osmotic, UV-B, heavy metals etc.) and have been accumulated. Experimental studies that profiled stress responsive pathways in plants (3) and computational studies on gene regulation (4) have utilized the data compiled in STIFDB. In a similar way the updated version of database: STIFDB2 will be useful for a wider community of researchers for detailed exploration of stress regulome in plants and its downstream functional and metabolic characteristics.

Acknowledgements

The authors thank UAS (B) and NCBS, TIFR for infrastructural support. MN acknowledges University Grant Commission (UGC), New Delhi, India, for the Senior Research Fellowship during the course of this research work.

References

1. Shameer, K., Ambika, S., Varghese, S.M., Karaba, N., Udayakumar, M. and Sowdhamini, R. (2009) STIFDB-Arabidopsis Stress Responsive Transcription Factor DataBase. Int J Plant Genomics, 2009, 583429.

2. Sundar, A.S., Varghese, S.M., Shameer, K., Karaba, N., Udayakumar, M. and Sowdhamini, R. (2008) STIF: Identification of stress-upregulated transcription factor binding sites in Arabidopsis thaliana. Bioinformation, 2, 431-437.

3. Babitha, K.C., Ramu, S.V., Pruthvi, V., Mahesh, P., Nataraja, K.N. and Udayakumar, M. (2012) Co-expression of AtbHLH17 and AtWRKY28 confers resistance to abiotic stress in Arabidopsis. Transgenic Res.

4. Georgii, E., Salojarvi, J., Brosche, M., Kangasjarvi, J. and Kaski, S. (2012) Targeted retrieval of gene expression measurements using regulatory models. Bioinformatics, 28, 2349-2356.



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