I want to annotate each gene in the Homo sapiens taxon with its respective GO terms and its hierarchical parent terms in the GO database. How can I systematically do that? While I am aware that the obo file contains information such as "is a," "part of," and "regulates," it lacks a comprehensive hierarchy from child GO terms to all their parent terms. Is there an existing method available to achieve this systematic annotation, or do I need to develop a custom script to extract this information from the obo file?
Yes, there are existing methods and tools that can help annotate genes to their direct Gene Ontology (GO) term and all their parent terms in the GO database. One widely used approach is called "GO term enrichment analysis" or "GO mapping."
GO mapping tools use statistical methods to identify enriched GO terms associated with a set of genes. These tools take a list of genes as input and systematically assign them to their corresponding GO terms and parent terms. They consider the hierarchical structure of the Gene Ontology to ensure that all relevant parent terms are included.
Some popular tools for GO term enrichment analysis and gene annotation include:
These tools typically provide a user-friendly interface where you can upload your gene list and obtain the annotated results, including direct GO terms and their parent terms.
Dear Mohammad Shahbaz Khan
Thank you for your response. However, I would like to clarify my objective. I am not looking to perform an enrichment analysis. Instead, I am interested in systematically building a hierarchical structure for each individual gene by annotating them with their respective Gene Ontology (GO) terms and their parent terms in the GO database.
I appreciate any further insights or suggestions you may have regarding this specific goal.
Thank you.
Mohammad Shahbaz Khan Certainly! Although the data is currently presented in Gene Ontology (GO) format, I want to create a comprehensive graph that visualizes the entire information. Further, I intend to annotate each gene with its corresponding GO term, including all parent terms associated with each gene.
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