Hi, I have three lists of genes, the number of identity of genes are not exactly same in each list. And each gene has its own expression value or relationship. I would like to know which two lists with expression values are closer or more similar. How can I get the answer? Which bioinformatic tool can I use?
What do you mean by "more similar'? Which pair of lists share the most statistically significant genes? Which lists share the most genes with similar expression levels? If that is all, you can align the lists by gene, take the common subset, then do something simple like a Wilcoxon Signed Rank test of each pair-wise set of lists (using your estimated expression levels, or if by significance, by their -log10pValues)..
If you mean functionally similar genes, you could do simultaneous functional ontology enrichment on them and look for overlap in the significantly enriched ontology or pathways. Commercial sites like GeneGO or Ingenuity will do this for you and compute the hypergeometric overlap and significance of the enriched pathways (e.g. GeneGo will rank and color code the enriched pathways by similarity). Both companies offer free trials of their web tools.
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