BMC Genomics 2009, 10:415 http://www.biomedcentral.com/1471-2164/10/415 VFeignunrdeia1gram depicting exclusive and overlapping CaESTs Venn diagram depicting exclusive and overlapping CaESTs. The numbers signify ESTs specific to the suscepti- ble and resistant genotypes and common between them. BLAST, an inferred putative function was assigned to the sequences and were sorted into various functional catego- ries as shown in Figure 2. We were able to assign function to 60% of the genes while our data analysis revealed that 18.28% of the CaUnigenes belong to no significant homology (NSH) class. In addition, 18.33% and 3.47% of the unigenes matched with hypothetical and unknown proteins respectively. Genes were assigned to the func- tional classes according to their biochemical function using gene function databases like GO http://www.gene ontology.org, metacyc http://www.metacyc.org and COG http://www.ncbi.nlm.nih.gov/COG. However, the classi- fication of transcripts is only tentative, since the biological function of many genes identified has not yet been estab- lished experimentally. The distributions of ESTs into diverse functional classes as shown in additional file 3 are described below. Genes involved in regulatory pathways (cell signaling and transcription and RNA processing and modification) Genes involved in cell signaling, transcription and RNA processing are known to regulate many cellular responses in an organism. Our data showed the presence of different types of protein kinases in both susceptible and tolerant chickpea genotypes. While serine/threonine protein kinase (contig86), Serine/threonine protein kinase active site (CaF1_JIE_03_A_05) and somatic embryogenesis receptor-like kinase were present only in the susceptible genotype; flag-tagged protein kinase domain of putative MAPKKK and protein kinase (CaF1_WIE_51_C_11) were found in the resistant one. Protein kinases are involved in disease response via a signaling cascade presumably con- served in plants, insects and mammals [23] while somatic embryogenesis related kinases are associated with brassi- nosteroid signaling pathway that plays a key role in plant defense [24]. The EST data revealed many components of FFuignuctrieon2al classification of CaUnigenes from root transcriptome Functional classification of CaUnigenes from root transcriptome. The genes identified were grouped into 23 func- tional classes as shown in the piechart based on metacyc, KOG and GO databases. The values represent the percentage of uni- genes assigned to a particular functional class. Page 4 of 21 (page number not for citation purposes)