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STIFDB [Stress Responsive TranscrIption Factor Database] :

STIFDB [Stress Responsive TranscrIption Factor Database] is a comprehensive collection of abiotic stress responsive genes in Arabidopsis thaliana, with options to identify probable Transcription Factor Binding Sites in their promoters. In the response to abiotic stresses like drought, cold, salinity, high light, heat, etc, ten specific families of transcription factors are known to be involved. HMM-based models are used to identify binding sites of transcription factors belonging to these families. We have also consulted literature reports to cross-validate the Transcription Factor Binding Sites predicted by the method.


STIFDB: Database Content:
Database contains various Stress Responsive Genes & Transcription Factor Binding Site Related Information :

TFmapTAIR Accession IDGene Names [Including Aliases]Chromosome PositionReferences to Publication and Related ResourcesTranscription Factor Family NameBinding SitesOrientation of Binding SitesStress-SignalZ-Score,  and Normalization Score


STIFDB: Database Statistics:
STIFDB: Database Statistics as on November 2008

Reference:
  • S. Ambika, Susan Mary Varghese, K. Shameer, M. Udayakumar and R. Sowdhamini (2008) STIF: Hidden Markov Model-based search algorithm for the recognition of binding sites of Stress-upregulated TranscrIption Factors and genes in Arabidopsis thaliana. Bioinformation, 2(10):431-437 [PMCID: PMC2561162]
  • Elizabeth A. Bray, (2002). Annals of Botany 89:803-811.
  • Stajich JE et.al., (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res, 12. 1611-1618.
  • Altschul, S.F. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.


Contact:
Prof. R. Sowdhamini [mini@ncbs.res.in]
Prof. M. Udayakumar

STIFdb Team:
Prof. R. Sowdhamini
Prof. M. Udayakumar
K. Shameer
S. Ambika
Susan Mary Varghese