J2: Annotation sources

Objective

• Find and select an annotation source for human genes by reading literature.
• Gather information on the dataset according to the questions detailed in this journal assignment.
• Summarize how the annotation source contributes to the functional annotation of genes.

Started: 2023-02-25 | Completed: 2023-02-25
Estimated time: 2 hrs | Actual time: 1.5 hrs

Procedure and Results

My selected annotation source is PANTHER

1. What sort of data is it? What sort of information does it offer us?

   Protein Analysis THrough Evolutionary Relationships (PANTHER) is an online tool that is a comprehensive, annotated library of gene family phylogenetic trees used to classify and identify the function of gene products. Each phylogenetic tree is used to annotate each protein member of the family by its family and class, subfamily, orthologs, paralogs, function, and pathways. It offers 3 main types of software tools: protein classification, gene list analysis, and protein-coding variant analysis. It is part of the Gene Ontology (GO) Consortium and uses GO for function classification. It also collaborates with UniProt, InterPro, and Phylogenes. PANTHER allows us to get information on a query gene and can generate lists of genes that share a molecular function or participate in a biological pathway. We can also use this tool to analyze lists of genes, proteins, or transcripts by categories such as molecular function or cellular component.

2. When and where was it published? Was it published?

   PANTHER was first established in 1998 at Molecular Application Group. Since 2006, PANTHER has been regularly updated and published yearly to expand coverage, provide high-level classification, and increase the speed and resolution of data acquisition. As of February 24, 2023, PANTHER is currently on version 17.0.

3. Is this annotation set updated regularly or is it a static source?

   PANTHER is updated regularly, adding more genomes, genes, and GO terms. Updates also introduce new services and tools.

4. Where can I find this data? (link to the download web address or ftp site or publication where it can be found)

   This tool can be accessed through its web interface, PANTHER. Data can also be downloaded via ftp, found in the Downloads tab.

5. How is the data formatted and released? Does it exist in some sort of standard file format?

   Data is exported in tab-delimited TXT file format. This file can be opened in a text editor or a spreadsheet. The data has columns, allowing the user to sort genes by protein family, molecular function, or biological process.

6. What identifiers are associated with these annotations?

   PANTHER uses standard identifiers. A user can search by protein sequence and for genes, the official gene symbol (HGNC), Entrez Gene ID, and GenBank accession number are supported.

Conclusion

• PANTHER is a useful annotation tool that is regularly updated.
• It is designed to classify proteins and their genes for high-throughput analysis, with the aim to make genome-scale phylogenetics accessible.
• Its web-based interface is easy to navigate.

References

Geistlinger, L., Csaba, G., Santarelli, M., Ramos, M., Schiffer, L., Turaga, N., Law, C., Davis, S., Carey, V., Morgan, M., Zimmer, R., & Waldron, L. (2021). Toward a gold standard for benchmarking gene set enrichment analysis. Briefings in bioinformatics, 22(1), 545–556. https://doi.org/10.1093/bib/bbz158

Thomas, P. D., Kejariwal, A., Campbell, M. J., Mi, H., Diemer, K., Guo, N., Ladunga, I., Ulitsky-Lazareva, B., Muruganujan, A., Rabkin, S., Vandergriff, J. A., & Doremieux, O. (2003). PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. Nucleic acids research, 31(1), 334–341. https://doi.org/10.1093/nar/gkg115

Thomas, P. D., Ebert, D., Muruganujan, A., Mushayahama, T., Albou, L. P., & Mi, H. (2022). PANTHER: Making genome-scale phylogenetics accessible to all. Protein science : a publication of the Protein Society, 31(1), 8–22. https://doi.org/10.1002/pro.4218

Mi, H., & Thomas, P. (2009). PANTHER pathway: an ontology-based pathway database coupled with data analysis tools. Methods in molecular biology (Clifton, N.J.), 563, 123–140. https://doi.org/10.1007/978-1-60761-175-2_7