Computational protocol: Mechanisms of action of Coxiella burnetii effectors inferred from host-pathogen protein interactions

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Protocol publication

[…] We performed standard enrichment analyses for C. burnetii-interacting host proteins as described previously []. Briefly, the enrichment of Gene Ontology (GO) [] and Kyoto Encyclopedia of Genes and Genomes (KEGG) [] pathways was calculated in R by using the Bioconductor packages BioMart [] and KEGGgraph []. The background set of proteins for the GO analysis involved all constituent proteins from the human PPI network, and we used the complete GO tree annotation, excluding the root and the top two levels of GO terms. The background set of proteins for the KEGG enrichment analysis involved human proteins available in KEGGgraph that participated in at least one KEGG pathway. We used the Benjamini-Hochberg method [] to correct all obtained p-values (praw) to adjusted p-values (padj). […]

Pipeline specifications

Software tools BioMart, KEGGgraph
Databases KEGG KEGG PATHWAY
Application Genome annotation
Organisms Coxiella burnetii, Homo sapiens, Mus musculus
Chemicals Cholesterol