applying a critical Benjamini Hochberg FDR q value of 0 05 In o

applying a critical Benjamini Hochberg FDR q value of 0. 05. In order to com pare and summarize enriched GO terms, we aimed to identify common most speci?c GO terms for the sets of up and downregulated genes, and thus implemented the following algorithm in the Perl programming lan guage, Combine all enriched GO terms from the input sets, Reduce Tipifarnib R115777 redundancy from higher hierarchy terms by keeping only the most speci?c GO terms, For each remaining most speci?c GO term, check all parental GO terms, sorted by increas ing distance from the corresponding child term, for the presence in the input sets, If a parental GO terms is present in all input sets denote it as common most speci?c, if any other equally distant parental terms are present in all input sets, denote them as common most speci?c as well and continue with the next most speci?c GO term, If none of the parental GO terms are present in all input sets, denote the corresponding most speci?c GO term as non common most speci?c, After completing the analysis of all most speci?c GO terms, reduce redundancy from the set of common most speci?c terms by removing all their parental terms, Out put the sets of common most speci?c and non common GO terms.

Fishers exact test based enrichment analysis of Kyoto Encyclopedia of Genes and Genomes pathway and Pfam domain annotations were performed using in house developed Perl scripts. The Benjamini Hochberg FDR was controlled at 0. 05. KEGG pathway annotation for A. niger was downloaded from the KEGG homepage. Pfam domain annotation for A. niger was generated by analyzing the predicted proteome of A.

niger strain CBS 513. 88 with the PfamScan Perl script. Secretome analysis Sample pre treatment 8 ml of 100% trichloracetic acid was added to frozen ?ltrate samples, which were subsequently com pletely defrosted by shaking at 4 C. Precipitated proteins were spun down and washed twice with ice cold ace tone. Precipitated protein pellets were air dried, solubi lized in 8 M urea and diluted 10x with 100 mM NH4HCO3. Reduction, alkylation of cysteines and diges tion with trypsin were performed according to Thakur et al. Another aliquot of trypsine was added after overnight digestion followed by incubation for 3 hours at 37 C to ensure complete diges tion. Samples were acidi?ed to 1% formic acid.

LC MS MS analysis The protein digests were analyzed in triplicate on Cilengitide an Accela LTQ Velos, using a 85 min data dependent LC MS MS run, 0 80 min 5 40% B, 80 82 min 40 60% B, 82 83 min 60% B, 83 85 min contain 5% B. Peptide separation was achieved by 25 ul injection on a C18 column using a guard column at 50 C and a ?ow rate of 0. 4 ml min?1. The data dependent MS method consisted of an enhanced MS scan 300 2000 m z and MS MS on the top 10 peaks. Data analysis The peptide data sets were searched against the A. niger database, which was manually modi?ed to contain the sequences of trypsin and BSA, using the Sorcerer 2 Sequest search engine. The search opted for carbamidomethylation, oxida t

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