Protocol Update for Large-scale genome and gene function analysis with PANTHER Classification System (v.14.0)
By Huaiyu Mi, Anushya Muruganujan, Xiaosong Huang, Dustin Ebert, Caitlin Mills, Xinyu Guo, Paul D. Thomas. Nature Protocols, 2019
1,325 citations recorded by the source corpus.
The PANTHER classification system (http://www.pantherdb.org) is a comprehensive system that combines genomes, gene function classifications, pathways and statistical analysis tools to enable biologists to analyze large-scale genome-wide experimental data. The current system (PANTHER v.14.0) covers 131 complete genomes organized into gene families and subfamilies; evolutionary relationships between genes are represented in phylogenetic trees, multiple sequence alignments and statistical models (hidden Markov models (HMMs)). The families and subfamilies are annotated with Gene Ontology (GO) terms, and sequences are assigned to PANTHER pathways. A suite of tools has been built to allow users to browse and query gene functions and analyze large-scale experimental data with a number of statistical tests. PANTHER is widely used by bench scientists, bioinformaticians, computer scientists and systems biologists. Since the protocol for using this tool (v.8.0) was originally published in 2013, there have been substantial improvements and updates in the areas of data quality, data coverage, statistical algorithms and user experience. This Protocol Update provides detailed instructions on how to analyze genome-wide experimental data in the PANTHER classification system. Here the authors provide an update to their 2013 protocol for using the PANTHER classification system, detailing how to analyze genome-wide experimental data with the newest version of PANTHER (v.14.0), with improvements in the areas of data quality, data coverage, statistical algorithms and user experience.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/8a270829fc20daaf46f10bb42f317068c258b7f1
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Molecular Biology
- Anushya Muruganujan
- Huaiyu Mi
- Paul D. Thomas
- Dustin Ebert
- Tremayne Mushayahama
- Laurent-Philippe Albou
- Caitlin Mills
- John T. Casagrande
Citations in the corpus
- PANTHER: Making genome‐scale phylogenetics accessible to all (2021, methodology): “36 If users cannot find a genome they are interested in, they can request it from us directly using the PANTHER feed-back email provided on the website.”
- PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API (2020, methodology): “The gene list analysis tools enable users to upload lists of genes or proteins and perform statistical tests to find enriched functional classes in their list (2,3).”