Correlated genes. We examined the probe sets with the highest Pearson's correlation with the probe set associated to gene Phc1 in MOE430A, 1423212_at, described in Figures 1 and 2. The tables report the 10 probe sets with highest positive (left) and negative (right) correlation. Among the positively correlated genes we can find Pou5f1/Oct4, a well known embryonic stem cell marker.

Pattern of expression. If a probe set behaves as a marker for a subset of samples in StemBase (that is, its level of hybridization is distinctively higher in that subset of samples than in the rest) its link in the "Pattern" column in Figure 1 will lead to details on this marker-pattern. These include a histogram (as displayed) indicating the number of samples versus hybridization for the samples with high and low expression of the gene, respectively. In this case, the probe set for gene Phc1 (1423212_at) exhibits high expression in murine embryonic samples, P19 embryonic carcinoma and osteoblasts (blue), and low expression in hematopoietic, bone marrow, skin, muscle, mammary and retinal stem cells and derivatives (red).

Sample vs Gene output. The query used was: species "Mouse", Experiment identifiers "E95 E124", Gene symbols "phc1 m6pr klrg1" (three murine genes that are encoded in a region of chromosome 6). The two experiments selected comprise a total of eight samples, run in the Affymetrix MOE430A chip. The three genes are represented by four probe sets (two for gene M6pr). The numbers indicate the hybridization values reported for each probe set in each sample with background colour indicating MAS5 calls (pink for present, green for absent, white for marginal). The "Related Medline" column contains links to Medline abstracts related to each gene, coloured according to the legend at the top of the graphic: transcription factor functionality is indicated for Klrg1 and Phc1, as well as a relation to stem cells for M6pr and Phc1.

Genomic viewer. (A) Genomic view of SAGE data. Sample S332 is a SAGE library obtained from differentiated neural stem cells. The view using the UCSC Genome Browser displays three SAGE tags (grey) whose identifiers indicate their chromosome and start position (in the Mouse Genome assembly from February 2006, version mm8) followed by sense, number of mapping locations, and tag counts in the library. The RefSeq Genes track shows only one gene (of uncharacterized function) in the region. Two SAGE tags overlap with the 3'UTR of the gene suggesting the expression of this gene and of an anti-sense transcript to this gene, respectively. The leftmost tag suggests the expression of a second transcript downstream this gene consistent with the data shown in the spliced ESTs track. (B) Combined view of SAGE and microarray data. The view shows another region of murine chromosome 6, which encodes the three genes analyzed in Figure 1, indicated by the RefSeq genes track (blue): Klrg1, M6pr and Phc1. In addition to the data from the SAGE library displayed in part A of the figure, additional tracks show data from another two samples. Those are its counterpart SAGE library (S331, neural stem cells) and a sample of DNA microarray of embryonic stem cells undergoing differentiation (S127). All three samples suggest lack of expression of the Klrg1 gene in these tissues: no SAGE tags overlapping with it and probe set 1420788_at for a transcript of this gene indicates no gene expression (green). The other two genes are expressed in the conditions represented.