Gene Expression Resources

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Gene Expression Resources

• Donald Dunbar
• Molecular Physiology Group
• 1st June 2007

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Outline

• Why do we need them
• Electronic northerns
• Microarray data resources
• Other stuff

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Why do we need them

• Gene of interest
• Want to know
• Level of expression
• Extent of expression (tissue specificity)
• Expression in various conditions specifically
• Expression in various conditions generally
• Can use this to prioritise genes of interest

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Electronic northern

• Idea
• use cDNA/EST sequences in database
• count the number for each gene
• compare with total transcipts
• gives an estimate of abundance
• total counts
• total counts per million transcripts

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Electronic northern
Step 1 Find the gene record at Entrez at
NCBI http//www.ncbi.nlm.nih.gov/gquery/gquery.fcg
i
gene
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Electronic northern
Step 2 Find the Unigene record (clusters of
sequences a gene)
?.
unigene
or go straight to Unigene in Entrez or search
at http//www.ncbi.nlm.nih.gov/entrez/query.fcgi?
dbunigene
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Electronic northern
Step 3 Select the Expression Profile link
Expression Profile
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Electronic northern
Step 3 See the profile
Renin Electronic Northern
transcripts per million
transcripts/total
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Electronic northern
cyclophilin
GPR50
NMDA receptor
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Electronic northern

• -ve
• relies on a cDNA source being sequenced
• biased by number of reads
• low counts give strange ratios
• rare transcripts wont be seen
• ve
• free
• good general coverage

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Microarray resources

• Two main data repositories
• GEO at NCBI (USA)
• ArrayExpress at EBI (UK)
• Process
• search for gene
• or search for experiment

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Microarray resources
As before, get the Unigene record
GEO Profile
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Microarray resources
But just get all the experiments
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Microarray resources

• Searching GEO or Array express

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Microarray resources

• We now have lots of in-house data
• ACTH treated mice adrenals kidneys
• Fat and lean mice various tissues
• HSD1 ko and wild type mice fat beds
• MR transgenic and wild type mice hippocampus
• Human dendritic cell lines with treatments
• Human Burkitts lymphoma cells
• Could be made available as a resource
• gene by gene analysis

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Microarray resources
Renin expression profiles
ACTH and low salt adrenals
MR transgenic hippocampus
ACTH kidneys
HSD1 ko fat beds
Fat and lean mice
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Microarray resources

• Full datasets have been made available
• GNF Symatlas (http//symatlas.gnf.org/SymAtlas/)

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Microarray resources

• Repositories ve
• no control over whats there
• GEO not so good, ArrayExpress better
• Repostories ve
• free
• can give some nice insights
• will get better as time goes on
• our in-house data can be very useful

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Other resources

• Mouse Genome Database
• http//www.informatics.jax.org/menus/expression_me
  nu.shtml

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Other resources

• Edinburgh Mouse Atlas (http//genex.hgu.mrc.ac.uk/
  )

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Other resources

• CGAP SAGE Genie (http//cgap.nci.nih.gov/SAGE/mSEM
  /)

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Web Page

• http//www.bioinf.mvm.ed.ac.uk/projects/gene_expre
  ssion.html

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Conclusion

• A gene of interest
• Resources to estimate its expression
• sequence based (eNorthern)
• microarray data
• Web page
• http//www.bioinf.mvm.ed.ac.uk/projects/gene_expre
  ssion.html
• See a link on the bioinformatics front page