- I presented a small analysis on The Arabidopsis lemone run. Stefanie found that some genes with a high pearson correlation coef (pcc) were not clustered together in the lemone output.I checked that on a large scale and found that indeed 90% of the genes pairs with a (absolute value) pcc > 0.9 are not in the same tight cluster. We came to the conclusion that it is probably because the matrix was not centered and scaled. I'm trying now another run with the very same matrix centered and scaled. - Yvan talked about the text mining challenge he's going to tackle with Sofie. We've been mentioning the possibility of applying the tools they have to extract Arabidopsis Knowledge, particularly protein-protein interactions. One of the problems is of course to validate the extraction, which could be tackled by using core cell cycle genes, for which we have extensive knowledge, as some kind of a reference set. - Anagha presented briefly the status of her work on yeast regulatory motifs. We discussed some possible strategies to find a biological meaning to the motifs that are over-represented, something that is not straightforward. That's about it, if I remember correctly. Eric Yves Van de Peer wrote:
Eric Bonnet wrote:
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any interesting conclusions ... I could not join because of staff meeting!
Thanks,
Yves