Tue, 09/23/2014
Tue, 09/09/2014 at 12:05 PM
Customer: I have a small transcriptional profiling project data set which I need help analyzing. The steps would include different approaches to define differentially expressed genes in a two factor design experiment using Agilent single color arrays. Then functional annotation from the host genes (Danio rerio) to equivalent mammalian genes to better understand likely biological functions.
Tue, 09/23/2014 at 5:13 PM
AccuraScience LB: Zebrafish is a model organism with genes well annotated. What might be the purposes of annotate these genes again in the context of comparing them with mammalian equivalents?
Tue, 09/23/2014 at 9:03 PM
Customer: The vast majority of Zebrafish studies are developmental and done in embryos so yes there is a lot of annotation and this was the reason for using this "model' organism originally. However, using the annotations provided by Agilent for their probes a lot of the genes had little functional annotation and a bit more work needed to be done to find any information on likely function in mammalian homologues... The other things is that there are some gene duplications in Zebrafish relative to the function of our interest, which might be important in drawing conclusions...
Wed, 09/24/2014 at 9:36 AM
AccuraScience LB: Here is the scope of work that we would propose that we do: (1) differential expression analysis involving the Agilent arrays, in all combinations of comparison you would like to do, and (2) Annotation of the Zebrafish genes of interest, in the context of comparison with mammalian gene equivalents, which involves the testing of ~3 ortholog gene-determining strategies, including Inparanoid, OrthoMCL and perhaps KOG and/or orthostrapper (very likely some of them will not work - this is part of the uncertainty involved in this project, and we won't know until we dig into it...), and present the results in an easy-to-interpret format.
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Note: LB stands for Lead Bioinformatician. An AccuraScience LB is a senior bioinformatics expert and leader of an AccuraScience data analysis team.
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