Median plots of identified SAGE tag -means cluster analysis using 14 clusters

We clustered 2, 536 SAGE tags with a count greater than 4 in one of the SAGE libraries and with a minimum specificity of 0.002 and that map unambiguously to a specific transcript or genome location into 14 clusters using -means clustering using a PoissonC algorithm as described in the Materials and methods. The median normalized tag counts for the tags in each of the clusters is shown plotted against the indicated SAGE libraries. The libraries shown include: EGFP+ TS17 (P+ TS17); EGFP+ TS19 (P+ TS19); EGFP- TS20 (N- TS20); EGFP+ TS20 (N+ TS20); EGFP+ TS21 (N+ TS21); EGFP+ TS22 (N+ TS22); whole pancreas TS22 (WTS22); whole pancreas TS26 (WTS26); adult isolated ducts (Ducts); adult isolated islets (Islets). A full list of the tags, the cluster they belong to, and their counts in each of the libraries is shown in Additional data file 2.<p><b>Copyright information:</b></p><p>Taken from "Identification of transcripts with enriched expression in the developing and adult pancreas"</p><p>http://genomebiology.com/2008/9/6/R99</p><p>Genome Biology 2008;9(6):R99-R99.</p><p>Published online 14 Jun 2008</p><p>PMCID:PMC2481431.</p><p></p

SOTA clustering of temporal expression profiles from qRT-PCR analysis of 44 genes in pancreas development

qRT-PCR was used to determine the relative expression levels of the indicated genes during pancreas development at the TSs indicated. The relative level of expression of each gene was normalized and a SOTA analysis used to group the genes. Heatmaps of the relative expression levels of the genes in the SOTA groups, including the SOTA centroid, with peak expression in the islets, the TS26 developing pancreas, the TS21-TS26 developing pancreas, or the ducts are shown. The data shown are averages of the results obtained from pancreases from three separate litters (pancreases from an individual litter were pooled) or islet/duct collections with triplicate reactions from the separate RNA extractions.<p><b>Copyright information:</b></p><p>Taken from "Identification of transcripts with enriched expression in the developing and adult pancreas"</p><p>http://genomebiology.com/2008/9/6/R99</p><p>Genome Biology 2008;9(6):R99-R99.</p><p>Published online 14 Jun 2008</p><p>PMCID:PMC2481431.</p><p></p

Representative staining patterns for genes expressed in each of the identified expression profiles

Representative genes for each of the identified spatial expression profiles, including genes with known and previously un-described, or novel, staining profiles in pancreas development, are shown. For this, images of hybridization staining patterns for whole embryo sagittal sections were obtained from the website and magnified to show the pancreas (outlined in red). Relevant probe IDs can be found in Additional data file 4.<p><b>Copyright information:</b></p><p>Taken from "Identification of transcripts with enriched expression in the developing and adult pancreas"</p><p>http://genomebiology.com/2008/9/6/R99</p><p>Genome Biology 2008;9(6):R99-R99.</p><p>Published online 14 Jun 2008</p><p>PMCID:PMC2481431.</p><p></p

Heatmap of SAGE tag counts for genes with known expression profiles in pancreas development

Tags for genes with well characterized expression profiles in pancreas development were identified and their normalized counts obtained in each of the ten SAGE libraries created. A heatmap, generated using the multi-experiment viewer as described in the Materials and methods, of these results is shown based on the counts of the tags per hundred thousand (TPH). SAGE tags used include: TACACGTTCTGACAACT (); AAGTGGAAAAAAGAGGA (); TAGTTTTAACAGAAAAC (); ACCTTCACACCAAACAT (); AATGCAGAGGAGGACTC (); CAGGGTTTCTGAGCTTC (); TCATTTGACTTTTTTTT (); GATTTAAGAGTTTTATC (); CAGCAGGACGGACTCAG (); CAGTCCATCAACGACGC (); AGAAACAGCAGGGCCTG (); GACCACACTGTCAAACA (); CCCTGGGTTCAGGAGAT (); TTGCGCTTCCTGGTGTT (); ACCACCTGGTAACCGTA (); GCCGGGCCCTGGGGAAG (); CTAAGAATTGCTTTAAA (); GCCCTGTTGGTGCACTT (); TCCCGCCGTGAAGTGGA (). The libraries shown include: EGFP+ TS17 (P+ TS17); EGFP+ TS19 (P+ TS19); EGFP- TS20 (N- TS20); EGFP+ TS20 (N+ TS20); EGFP+ TS21 (N+ TS21); EGFP+ TS22 (N+ TS22); whole pancreas TS22 (WTS22); whole pancreas TS26 (WTS26); adult isolated ducts (Ducts); adult isolated islets (Islets).<p><b>Copyright information:</b></p><p>Taken from "Identification of transcripts with enriched expression in the developing and adult pancreas"</p><p>http://genomebiology.com/2008/9/6/R99</p><p>Genome Biology 2008;9(6):R99-R99.</p><p>Published online 14 Jun 2008</p><p>PMCID:PMC2481431.</p><p></p

Specificity threshold accurately predicts spatial expression restriction

A plot of specificity (S) versus cumulative tag types represented shows the distribution of tags into tags with high (S > 0.1; top), medium (0.001 > S < 0.1, middle), and low (S < 0.001, bottom) S values. Representative hybridization staining patterns from TS22 whole embryo saggital sections obtained from are shown for each specificity group. Relevant probe IDs can be found in Additional data file 4. Arrows indicate the location of the pancreas (p).<p><b>Copyright information:</b></p><p>Taken from "Identification of transcripts with enriched expression in the developing and adult pancreas"</p><p>http://genomebiology.com/2008/9/6/R99</p><p>Genome Biology 2008;9(6):R99-R99.</p><p>Published online 14 Jun 2008</p><p>PMCID:PMC2481431.</p><p></p