10 Current Genomics, 2009, 10, 10-17 Comparative Analyses of Plant Transcription Factor Databases Silvia R. Ramirez and Chhandak Basu* School of Biological Sciences, University of Northern Colorado, Greeley, Colorado, USA Abstract: Transcription factors (TFs) are proteinaceous complex, which bind to the promoter regions in the DNA and af- fect transcription initiation. Plant TFs control gene expressions and genes control many physiological processes, which in turn trigger cascades of biochemical reactions in plant cells. The databases available for plant TFs are somewhat abundant but all convey different information and in different formats. Some of the publicly available plant TF databases may be narrow, while others are broad in scopes. For example, some of the best TF databases are ones that are very specific with just one plant species, but there are also other databases that contain a total of up to 20 different plant species. In this re- view plant TF databases ranging from a single species to many will be assessed and described. The comparative analyses of all the databases and their advantages and disadvantages are also discussed. Received on: September 15, 2008 - Revised on: October 9, 2008 - Accepted on: October 11, 2008 Key Words: Plant transcription factor databases, bioinformatics. INTRODUCTION Transcription factors (TFs) play many important roles in plant developmental processes and plant responses to the change in environments [1]. The complete sequencing of Arabidopsis thaliana [2] and the rice (Oryza sativa) [3] ge- nomes have propelled the ongoing research on plant molecu- lar genetics and genomics. There are many new and power- ful genomic tools [4] to power the research in the field of plant genomics and proteomics. It is crucial that important information is gathered about the plant cellular, biochemical, and molecular processes that drive the responses to the change in the environment in plants, and TFs databases are precisely a tool that aids in this ongoing research. Databases for Arabidopsis thaliana are most extensive than for any other plant. In this review, we presented a comparative analysis of several publicly available plant TF databases. To use the information presented here most effectively, the readers are encouraged to browse the respective TF database websites when reading this article. All website names, data- base and bioinformatics tools abbreviations mentioned throughout this paper have been explained in Table 1 unless they are explained in parentheses. This review will explore different TF databases and assess overall strengths and weaknesses of each and Table 2 summarizes the overviews of the plant TF databases. RARTF: RIKEN ARABIDOPSIS FACTOR DATABASE (JAPAN) TRANSCRIPTION The RARTF: RIKEN Arabidopsis Transcription Factor Database (http://rarge.gsc.riken.jp/rartf/) is a database only for Arabidopsis thaliana TFs [5]. This database is organized in table like manner including the TF ID, TF family, and the *Address correspondence to this author at the School of Biological Sci- ences, 2480 Ross Hall, University of Northern Colorado, Greeley, Colorado 80639, USA; Tel: 1-970-351-2716; Fax: 1-970-351-2335; E-mail: chhandak.basu@unco.edu number of TF members in each family. The website has a position specific interative BLAST or PSI-BLAST search feature which allows to search for distantly related protein families. If specifically looking for a TF of Arabidopsis thaliana then this database should be a great resource. How- ever, if searching for a database that can compare across different species, then it would not be as helpful. The table setup at the opening page of the website is user friendly be- cause all TF family can be browsed and accessed from the main homepage. In addition to that, the other search tools are right below the TF table where they are easily seen. The con- tent of the website includes the table of all TFs, reverse PSI- BLAST search, BLAST search, PSI- BLAST search, and retrieve FASTA format sequence file. Some of the great fea- tures of the database are inclusion of the motif of TFs and full-length cDNAs associated with each gene coding for the TF. If a TF is selected from the database table, it redirects to another table that contains the gene IDs that then provide gene code, gene name, e-value, transposon mutants, RAFL, and genome map. In addition to the well organized data pro- vided, the website contains direct links to other plant genome information websites/databases like TIGR, TAIR, and MIPS. It should be mentioned here that The Institute of Genomic Research (TIGR), USA has merged with J. Craig Venter Research Institute (JCVRI), USA. So, it is time to the change the TIGR link to JCVRI link. The minor error that needs attention is when the reverse PSI-BLAST link is selected an error message appears which states, “You don't have permis- sion to access /rartf/rps_blast/ on this server”. The website does not have downloads which are part of other databases, and there is no link to directly contact the developers if needed. On the main homepage there are additional links to the RIKEN Arabidopsis Genome Encyclopedia: RARGE and to the Arabidopsis Gene Regulatory Information Server: agris (Ohio State University, USA). The website was last updated in July 20, 2006. Overall this is an effective data- base for Arabidopsis thaliana TFs. 1389-2029/09 $55.00+.00 ©2009 Bentham Science Publishers Ltd.