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. 2016 Jul 29;16(1):169.
doi: 10.1186/s12870-016-0860-y.

CicerTransDB 1.0: a resource for expression and functional study of chickpea transcription factors

Saurabh Gayali  1 , Shankar Acharya  1 , Nilesh Vikram Lande  1 , Aarti Pandey  1 , Subhra Chakraborty  1 , Niranjan Chakraborty  2
Affiliations

CicerTransDB 1.0: a resource for expression and functional study of chickpea transcription factors

Saurabh Gayali et al. BMC Plant Biol. .

Abstract

Background: Transcription factor (TF) databases are major resource for systematic studies of TFs in specific species as well as related family members. Even though there are several publicly available multi-species databases, the information on the amount and diversity of TFs within individual species is fragmented, especially for newly sequenced genomes of non-model species of agricultural significance.

Description: We constructed CicerTransDB (Cicer Transcription Factor Database), the first database of its kind, which would provide a centralized putatively complete list of TFs in a food legume, chickpea. CicerTransDB, available at www.cicertransdb.esy.es , is based on chickpea (Cicer arietinum L.) annotation v 1.0. The database is an outcome of genome-wide domain study and manual classification of TF families. This database not only provides information of the gene, but also gene ontology, domain and motif architecture.

Conclusion: CicerTransDB v 1.0 comprises information of 1124 genes of chickpea and enables the user to not only search, browse and download sequences but also retrieve sequence features. CicerTransDB also provides several single click interfaces, transconnecting to various other databases to ease further analysis. Several webAPI(s) integrated in the database allow end-users direct access of data. A critical comparison of CicerTransDB with PlantTFDB (Plant Transcription Factor Database) revealed 68 novel TFs in the chickpea genome, hitherto unexplored. Database URL: http://www.cicertransdb.esy.es.

Keywords: Chickpea; Database; Food legume; Genome-wide; Transcription factor.

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Figures

Fig. 1
Fig. 1
Workflow of browsing features of CicerTransDB
Fig. 2
Fig. 2
Screenshot of the search page with description of various sections
Fig. 3
Fig. 3
Schematic diagram showing various tools and dataflow of CicerTransDB. *1 denotes data obtained by blast. *2 denote data derived from annotation
Fig. 4
Fig. 4
Venn diagram showing comparison of transcription factors in CicerTransDB with that in the PlantTFDB. The comparison reveals 68 new transcription factors in the chickpea genome which were previously unexplored
See this image and copyright information in PMC

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