Improve Research Reproducibility A Bio-protocol resource
Concise Method
tooltip

GO enrichment analysis.

KM Kaitlyn N. Myers
DC Daniel Conn
AB Amanda M. V. Brown
request Request a Protocol
ask Ask a question
Favorite

To determine functional overrepresentation in gene content and SNPs among Xiphinematobacter isolates, gene ontology (GO) enrichment analysis was performed on the Xiphinematobacter sp.-only pangenome not overlapping with outgroup Verrucomicrobia, designated “diff,” and the universe gene set included all genes in both sets. Full hierarchical GO annotations for the universe gene set were obtained primarily from UniProtKB and as needed from other databases (MetaCyc and KEGG). Enrichment analyses were performed in topGO v2.4.0 (96) which accounts for GO-term graph topology. TopGO was implemented in R using the script aip_topgo_usage.consider_universe.R (https://github.com/lyijin/topGO_pipeline/). Test statistics were assigned by the “weight01.fisher” algorithm for which returned P values are regarded as corrected (or not affected) by multiple testing. GO enrichment analysis in topGO was also performed on the genes with statistically significant DBGWAS SNPs associated with host Xiphinema phenotype as the filter on the complete Xiphinematobacter diff gene set in topGO.

Copyright and License information:  ©2021 Myers et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

post Post a Question
0 Q&A