Zhang et al. BMC Genomics 2011, 12:63 http://www.biomedcentral.com/1471-2164/12/63 Page 5 of 20 Figure 2 The MPSS signature abundance distributions. The abundance of each signature is calculated as a percentage of total signatures in the mutant (black column) and wild-type (gray column). the unigenes annotated by the BLAST search against the public protein and nucleotide databases (SwissProt, KEGG, COG, and Nr) where the E-value threshold was set at 1E-5. Of the 31,468 MT and 29,864 WT unigenes, 23,835 and 23,076 unigenes had at least one hit within these databases, respectively (Table 2). The remaining unigenes (24.26% and 22.73%, respectively) that were not annotated likely comprised citrus-specific genes, as well as genes with homologs in other species whose cor- responding biological functions have not yet been inves- tigated. In addition, proteins with the highest ranks in the BLAST results were taken to decide the coding region sequences of the unigenes, and the coding region sequences were then translated into amino sequences with a standard codon table. Consequently, both the nucleotide sequences (5’-3’) and amino sequences of the unigene coding region were acquired. Unigenes that cannot be aligned to any database were scanned by ESTScan [41] to get the nucleotide (5’-3’) and amino sequences of the coding regions. A total of 25,318 genes (12,064 in sense and 12,254 in antisense) were identified in the MT library (Additional File 2), and 22,510 genes (11,681 in sense and 11,892 in antisense) were identified in the WT library (Additional File 3); a total of 7,150 (22.72%) for the MT and 6,354 (21.28%) for the WT library were not identified in sense or antisense. Tran- scription factors (TFs) are important regulators for acti- vating or repressing the expression of coding or noncoding genes, through which they can further influ- ence or control many biological processes [42]. Putative TF genes were identified by a BLAST search against rice, Arabidopsis, and Citrus sinensis TF genes down- loaded from PlantTFDB (http://planttfdb.cbi.pku.edu. cn:9010/index.php) [43], identifying 569 putative TFs belonging to 60 TF families; there were 552 TFs in the WT library and 564 TFs in the MT library (Additional File 4). The MADS family was the most prevalent, fol- lowed by the AP2/EREBP and WRKY families. These results were slightly different from those of Arabidopsis [33] and rice [30], in which the AP2/EREBP family and zinc finger family were predominant, respectively. In addition, the AP2/EREBP family and C2H2 family were slightly differentially expressed between the genotypes (Additional File 4). Functional classification of differential expression genes As a result of the completed genomic sequencing of the plant Arabidopsis, the currently available expressed sequences have been invaluable in defining the correct components of the gene structure in this species [44]. To evaluate the potential functions of genes with signifi- cant transcriptional changes between the MT and WT, Gene Ontology (GO) categories were assigned to the significant 2735 genes based on the TAIR GO slim pro- vided by blast2GO. The categorization of differential expression genes according to the cellular component,