Romeuf et al. BMC Genomics 2010, 11:185 http://www.biomedcentral.com/1471-2164/11/185 Page 6 of 15 Table 1: Number of genes belonging to TF families identified in rice and wheat. (Continued) 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 MBF1 R1R2R3 R2R3 MYB-related NAC Nin-like NZZ ASH1 EZ RBCMT SUVAR TRX S1Fa-like TCP Trihelix TUB ULT Whirly Alfin C2C2-CO-like C2C2-DOF C2C2-GATA C2C2-YABBY C2H2 C3H HRT-like LIM PHD PLATZ SBP SRS VOZ ZIM WRKY Total 3 5 133 84 149 14 1 6 2 8 15 3 4 24 23 21 2 1 13 54 36 23 12 113 90 1 13 79 20 28 6 2 29 113 31 7 164 159 188 16 0 12 7 16 44 19 11 19 36 41 1 5 25 119 25 47 20 139 169 2 37 243 25 21 0 7 95 156 688 14 702 1082 1226 71 0 61 46 187 266 106 479 58 175 308 9 58 196 820 148 221 303 975 1378 6 591 1586 185 160 0 36 1076 687 46 6 165 114 193 14 3 13 8 26 38 5 12 11 21 36 0 6 24 120 34 31 11 123 129 1 36 170 20 23 1 3 86 177 77 13 329 273 381 30 3 25 15 42 82 24 23 30 57 77 1 11 49 239 59 78 31 262 298 3 73 413 45 44 1 10 181 333 42 5 203 116 269 14 3 9 3 23 51 10 23 14 57 63 1 11 25 81 28 25 30 122 169 3 39 126 33 15 1 10 13 187 2384 3790 27916 3322 7112 3820 a number of tentative consensus contigs (TCs) b number of sequences in TCs c number of unique sequences corresponding to wheat TFs in wDBTF d number of TFs with DNA-binding domain. For GRF, LUG, NZZ, Trihelix, ULT, Whirly, HRT-like and VOZ subfamilies no DNA-binding domain sequences are available in the Pfam database, so their attribution to a TF subfamily depended on their similarity to respective member sequences from rice database. large TF subfamilies in wheat are the EREBP, AUX/ IAA, bHLH, R2R3-MYB, bZIP, WRKY and C3H zinc finger families each with more than 150 members. At the other extreme, three subfamilies (LFY, SRS and LS) are each represented by a single gene. Wheat appears to have more AUX/IAA, CCATT-Dr1, HMG, MBF, S1Fa-like, Whirly and VOZ genes than would be pre- dicted by comparing the number of genes proportion- ally to the number in rice, i.e. more than three times more. For each TF subfamily, a web page is available listing all accession numbers either for contigs or singletons. Wheat TF expression in silico Almost 50% of sequences identified as wheat TFs are singletons and the majority (70%) of wheat TF contigs are made up of 2-5 ESTs. For all the families, the aver- age number of ESTs per contig is 6.8. This suggests that wheat TFs, like other plant TFs, are not highly expressed. By referring to the source of the material used to make each EST library, in silico expression data for each accession was compiled and is provided in the database. We found 4,305 wDBTF wheat sequences are repre- sented on the Affymetrix wheat genome array using