User:Matthew Whiteside/Notebook/Fumigatus Microarray/2009/01/23
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Fumigatus Task 1.1
Email to margo:
In our last meeting, Margo you gave me a list of pathways and functions to look into, in more detail. That list was:
1. polyketide synthase 2. PABA 3. Uracil / Uridine 4. Transporters 5. Gliotoxin 6. Siderophore biosynthesis
I looked manually into each of these functions, recording:
a) A. nidulans genes from the list i obtained from the David et al. paper that were involved in that function, b) if those genes had A. fumigatus orthologs, & c) whether those A.fumigatus orthologs were differentially-expressed in the microarray data.
Gliotoxin and siderophore biosynthesis were not annotated in the David et al list, so i found the genes related to those functions by searching the TIGR A. fumigatus database's annotations.
I've attached a document with the results of my search, but here is a brief summary: most of the A. fumigatus genes were not differentially expressed. In the list of functions above, I found 5 genes differentially-regulated:
1. Afu2g08460, pseudouridylate synthase is up-regulated (1 of 9 genes annotated in Uracil / Uridine group). 2. Afu1g10930, ammonium transporter is up-regulated (1 of 9 transporters in David et al. list) 3. Afu6g09710, gliotoxin efflux transporter GliA and Aflu1g13370, B1-aldehyde reductase are up-regulated (2 of 28 genes in gliotoxin biosynthesis group). 4. Afu3g03390, siderophore biosynthesis lipase/esterase is up-regulated (1 of 12 genes in siderophore biosynthesis group).
I was surprized not to see more siderophore genes up-regulated. For instance SidA (Afu2g07680) was not up-regulated. I think I should double-check the expression data that I have. Jason, can i get the full dataset from you, so i can double-check what i have.