Susi+Ideas

Ideas to think about:

- CHANGE HYPOTHESIS: mut-p53 does not regulate Dicer, hence: --> look at the OVERALL expression rate of all miRNA in the small RNA seq data to show that there is no reduction of miRNA this is doable in fact we can show this from our current data analysis itself. (Carries Idea: use the RPM values which have been normalized to take into account the different overall sequencing depth of the libraries. using the number of reads will not take that into account) This is not true. The total read count takes sequencing depth of each sample into account when making the differential comparison with edgeR or DESeq.

- link miRNA data to Long RNA data (the latter should be less noisy than iTRAQ) this is also doable (8 hours)

- only link a pre-sepcted list of miRNA to iTRAQ or RNAseq (mir10b, mir-155, mir-181b) this can be done once we decide the preselected list, is it just the 3 above?

- look at the expression levels of all phosphatases to identify potential phosphatases for pMKK4 this I do not have an idea about. Can you please clarify a little more about this? What do you mean by phosphatases? What is the hypothesis?

- create a heat map of the expression values for all integrins (based on long RNA seq) - ITGa1 ITGa2 ITGa2b ITGa3 ITGa4 ITGa5 ITGa6 ITGa7 ITGa8 ITGa9 ITGa10 ITGa11 ITGaD ITGaE ITGaL ITGaM ITGaV ITGaX ITGb1 ITGb2 ITGb3 ITGb4 ITGb5 ITGb6 ITGb7 ITGb8

this I can do tomorrow before I leave for the conference. 1 hour.