BMC Genomics 2004, 5:54 http://www.biomedcentral.com/1471-2164/5/54 Table 4: Top 20 contigs with the most assembled ESTs. Contig ID # ESTs Best Human Match E-value MexCluster_4615_Contig1 MexCluster_600_Contig1 MexCluster_6279_Contig1 MexCluster_10867_Contig1 MexCluster_5357_Contig1 MexCluster_9285_Contig3 MexCluster_7987_Contig3 MexCluster_9285_Contig1 MexCluster_9279_Contig3 MexCluster_11203_Contig1 MexCluster_8737_Contig2 MexCluster_3193_Contig1 MexCluster_8737_Contig7 MexCluster_5005_Contig3 MexCluster_6225_Contig1 MexCluster_1066_Contig1 MexCluster_8737_Contig4 MexCluster_8187_Contig2 MexCluster_2761_Contig1 MexCluster_9187_Contig1 A. t. tigrinum TigCluster_6298_Contig1 TigCluster_10099_Contig2 TigCluster_6470_Contig1 TigCluster_9728_Contig2 TigCluster_6594_Contig1 TigCluster_5960_Contig1 TigCluster_7383_Contig1 TigCluster_6645_Contig1 TigCluster_7226_Contig4 TigCluster_7191_Contig1 TigCluster_10121_Contig1 TigCluster_6705_Contig1 TigCluster_7854_Contig1 TigCluster_6139_Contig1 TigCluster_7226_Contig2 TigCluster_10231_Contig1 TigCluster_6619_Contig1 TigCluster_7232_Contig2 TigCluster_5768_Contig1 TigCluster_9784_Contig3 415 354 337 320 307 285 252 240 218 181 152 145 134 132 125 122 114 113 109 105 654 193 167 142 117 91 77 76 74 67 64 63 62 52 51 44 36 35 34 32 (NM_000519) delta globin (NM_182985) ring finger protein 36 isoform a (NM_000559) A-gamma globin (NM_000558) alpha 1 globin (NM_000558) alpha 1 globin (NM_001614) actin, gamma 1 propeptide (NM_001402) eukaryotic translation elongation f1 (NM_001101) beta actin; beta cytoskeletal actin (NM_000223) keratin 12 (NM_002032) ferritin, heavy polypeptide 1 (NM_058242) keratin 6C (NM_004499) heterogeneous nuclear ribonucleoprotein (NM_058242) keratin 6C (NM_031263) heterogeneous nuclear ribonucleoprotein (NM_001152) solute carrier family 25, member 5 [31015660] IMAGE:6953586 (NM_058242) keratin 6C; keratin, epidermal type II (NM_005507) cofilin 1 (non-muscle) (NM_001961) eukaryotic translation elongation factor2 (NM_007355) heat shock 90 kDa protein 1, beta (NM_000519) delta globin (NM_001614) actin, gamma 1 propeptide (NM_000558) alpha 1 globin (NM_000477) albumin precursor (NM_001402) eukaryotic translation elongation f1 (NM_001101) beta actin; beta cytoskeletal actin (NM_001614) actin, gamma 1 propeptide (NM_001063) transferrin (NM_006009) tubulin, alpha 3 (NM_019016) keratin 24 (NM_005141) fibrinogen, beta chain preproprotein (NM_000558) alpha 1 globin (NM_021870) fibrinogen, gamma chain isoform (NM_001404) eukaryotic translation elongation f1 (NM_006009) tubulin, alpha 3 (NM_003018) surfactant, pulmonary-associated prot. (NM_000041) apolipoprotein E (NM_003651) cold shock domain protein A (NM_003380) vimentin |XP_218445.1| similar to RIKEN cDNA 1810065E05 E-39 E-110 E-32 E-38 E-37 0 0 0 E-113 E-70 E-131 E-90 E-131 E-124 E-151 E-16 E-132 E-65 0 0 E-38 0 E-39 E-140 0 0 0 0 E-160 E-89 0 E-39 E-121 0 0 E-08 E-38 E-46 E-177 E-15 even when different contigs matched the same RefSeq ref- erence. In almost all cases, approximately the same number of matches was found per functional descriptor for both species. This was not simply because the same loci were being identified for both species, as only 20% of the total number of searched contigs shared sufficient identity (BLASTN; E<10-80 or E<10-20) to be potential homologues. In this sense, the sequencing effort between these two species was complementary in yielding a more diverse collection of ESTs that were highly similar to human gene sequences. Informatic searches for regeneration probes The value of a salamander model to regeneration research will ultimately rest on the ease in which data and results can be cross-referenced to other vertebrate models. For exam- ple, differences in the ability of mammals and salamanders to regenerate spinal cord may reflect differences in the way cells of the ependymal layer respond to injury. As is observed in salamanders, ependymal cells in adult mam- mals also proliferate and differentiate after spinal cord injury (SCI) [24,25]; immediately after contusion injury in adult rat, ependymal cell numbers increase and prolifera- tion continues for at least 4 days [[26]; but see [27]]. Rat ependymal cells share some of the same gene expression Page 5 of 17 (page number not for citation purposes)