User:Matthew Whiteside/Notebook/Fumigatus Microarray/2009/03/10
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Fumigatus Microarray DataStatistical TestsObtained the original data in form of TIGR MeV .anl project files from Jason (~/data/projects/a_fungus/2/ma_data) Project Description:
Comments:
Biological ValidationIn the paper "SreA-mediated iron regulation in Aspergillus fumigatus" <pubmed> 18721228 </pubmed>, found that SreA is a main regulator for iron uptake proteins (siderophore etc). Using the list of SreA response genes from this paper (49 in total incl SidA), I crossed ref the list of DE genes in response to low iron for the 3 time points (p 0.05) Common Genes 2h: 4 4h: 5 6h: 10 The list of SreA regulated genes are in ~/data/projects/a_fungus/2/ma_data/sreA_ko_study/sreA_reg_genes.pvals. linux command used: cut -f 12 sig_probes_4h_p005.txt | sort | join - sreA_reg_locus_tags.txt | uniq | wc -l (sreA_reg_locus_tags.txt already sorted) check overlap_* files for list of common genes.
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