Fig. 1. Volcano plot of the 4844 probe sets on our Affymetrix arrays that were tested for significant differences in hybridization intensity (transcript abundance) across time via ANOVA. Points below the dark horizontal line are not significant after adjusting the FDR to 0.001.

Fig. 2. Graphical representation of the gene ontologies for 123 probe sets. (a) The proportion of genes that fit into one, two, three, or four or more biological process categories. (b) The proportion of the 265 ontologies that fit into each category. The mean number of ontologies per gene = 2.15. (c) The number of genes that are located in each of the ontology categories. Some genes are in more than one category. (d) The proportion of genes that are in each category when genes are assigned to only one category. Assignments were made in decreasing order of priority from the following list (i.e., one is highest priority): (1) apoptosis, (2) development, (3) immune response, (4) detection of external stimulus, (5) response to stress, (6) cell adhesion, (7) cell organization and biogenesis, (8) cell communication, (9) cell cycle, (10) ion transport, (11) transport, (12) proteolysis, (13) metabolism, (14), physiological process, (15) unknown, (16) no hit in DAVID.

Fig. 3. Expression profiles of the two clusters obtained from the SOM algorithm. (a) Cluster 1 (up regulated) contains 61 genes. (b) Cluster 2 (down regulated) contains 62 genes. Gene names are given based on the best BLASTX hit to the human genome.

Fig. 4. Down-regulated keratins. The y-axis represents intensity (arbitrary units), and the x-axis represents days (0, 2, 12, 28). Gene names are given based on the best BLASTX hit to the human genome. Dark circles represent the mean of three samples ± S.E.

Fig. 5. Up-regulated keratins. The y-axis represents intensity (arbitrary units) and the x-axis represents days (0, 2, 12, 28). Gene names are given based on the best BLASTX hit to the human genome. Dark circles represent the mean of three samples ± S.E.

Fig. 6. RT-PCR of keratins. Columns represent 0, 2, and 12 days of T4 treatment.

Primers used for RT-PCR

Contig IDs represent curated salamander EST assemblies with F indicating the 5′ primer and R indicating the 3′ primer. Gene names represent the common name for the best human RefSeq protein sequence. GAPDH stands for the transcript glyceraldehyde-3-phosphate dehydrogenase.

Keratin probe sets evaluated by RT-PCR

List of 62 up-regulated genes showing best BLAST hits and expression levels

Sal IDs correspond to Ambystoma mexicanum contigs used for probe production. Sequence similarity was assessed using the entire contig sequence. Day 2, day 12, and day 28 columns are the average fold changes compared to day 0.

List of 61 down-regulated genes showing best BLAST hits and expression levels

Sal IDs correspond to Ambystoma mexicanum contigs used for probe production. Sequence similarity was assessed using the entire contig sequence. Day 2, day 12, and day 28 columns are the average fold changes compared to day 0.