Expression of Human Genes

The map shows all the Human exons for which reliable gene expression correlations can be calculated from GEO Affymetrix HG-U133 2+ GeneChip CEL files. It can be searched via a

• graphical interface (2.5 MBytes) (best with firefox 3) or via a
• list (6 MBytes) of all the human genes. This links to exon-exon correlations, correlation heat maps for probes within the same exon and information about the gene and its exons in Ensembl.
  Its quite nice to use links in rnanet.html to open gene_description.html in a separate windows. (Eg Firefox menu Edit|Preferences|Tabs new pages should be opened in a new window.) This allows the browser to scroll to each gene without reloading the whole file each time.

Additional screens:

• Scatter graphs of GEO probes (firefox). (Example)
       Scatter plot showing unexpected presence of mycoplasma (press plot) in 1% of GEO by using on human microarrays Aldecoa-Otalora, BioTechniques, Vol. 47, No. 6, pp1013-1016, December 2009, doi 10.2144/000113271, PDF . Affymetrix 1570561_at probes give a new way to detect contamination by these bacteria. Data from infected cell cultures perhaps aught to be excluded. (Drag crosshairs over suspect points to give links into description of RNA sample.)
• Correlation heatmaps between HG-U133 2+ probes in GEO. (Example)
• Contents of GEO by probeset.
  probeset.php? (add desired HG-U133 2+ probeset after question mark) Eg probeset.php?1556291_at, output.

Frequently asked questions
A Map of Human Gene Expression, W. B. Langdon, Technical report CES-486 Computing and Electronic Systems, University of Essex, UK, July 2008.
How to slides presented at UKAffy 2008.
From Functional Genomics to Systems Biology EMBO 2008 PDF.

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