Download A Gene Expression Experiment – Practical

A Gene Expression Experiment part II– Practical
November 2008
Richard Mott
1. Repeat the analysis of the liver and lung data set in the lecture
2. Look for sets of transcripts that have different patterns of expression between liver and
lung. For example, you might look for genes which are expressed in both tissues but are
not correlated, or look for genes expressed in one tissue but not the other. Perform GO
analyses on these sets of genes. Do you find anything interesting?
3. For the eQTL analysis on chromosome 19, identify those transcripts with cis eQTLs. You
will need to read in the file of genome locations of transcripts in
mouse.transcripts.genes.txt, and you will need to match the transcript names in that file
to you transcript names. To do this, you can modify the transcript names in the
annotation file using the R code
Transcripts <- paste(“LIVER.express”, make.names(transcripts), sep=””)
4. Once you have identified the cis eQTLs on chromosome 19 (use a logP threshold of say
4, and insist the eQTL peak is within 2Mb of the transcript location), use the file
All.Summary.010808.build37.txt to classify the eqTLs by SNP content. What do you find?