Large-scale gene function analysis with PANTHER Classification System

By Huaiyu Mi, Anushya Muruganujan, John T. Casagrande, Paul D. Thomas. Nature Protocols, 2013

2,397 citations recorded by the source corpus.

The PANTHER (protein annotation through evolutionary relationship) classification system (http://www.pantherdb.org/) is a comprehensive system that combines gene function, ontology, pathways and statistical analysis tools that enable biologists to analyze large-scale, genome-wide data from sequencing, proteomics or gene expression experiments. The system is built with 82 complete genomes organized into gene families and subfamilies, and their evolutionary relationships are captured in phylogenetic trees, multiple sequence alignments and statistical models (hidden Markov models or HMMs). Genes are classified according to their function in several different ways: families and subfamilies are annotated with ontology terms (Gene Ontology (GO) and PANTHER protein class), and sequences are assigned to PANTHER pathways. The PANTHER website includes a suite of tools that enable users to browse and query gene functions, and to analyze large-scale experimental data with a number of statistical tests. It is widely used by bench scientists, bioinformaticians, computer scientists and systems biologists. In the 2013 release of PANTHER (v.8.0), in addition to an update of the data content, we redesigned the website interface to improve both user experience and the system's analytical capability. This protocol provides a detailed description of how to analyze genome-wide experimental data with the PANTHER classification system.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c258d0814ac16455fa48f752c22b3bd4bdce03c1

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Citations in the corpus

Mutation severity spectrum of rare alleles in the human genome is predictive of disease type (2019, methodology): “001 ease) of GOfat biological process terms [101] and GO enrichment of PANTHER classification [102].”
PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools (2018, methodology): “PANTHER supports several tools for analyzing genes by functional classifications, which have been described in detail (9).”
YY1 Is a Structural Regulator of Enhancer-Promoter Loops (2017, positive): “…2016 https://pachterlab.github.io/kallisto/ Deseq2 Love et al., 2014 https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html PANTHER GO Mi et al., 2013, 2017 http://pantherdb.org Origami This study https://github.com/younglab/origami Cell Ranger 10X Genomics…”
Ensembl comparative genomics resources (2016, background): “Despite recent concerns on the orthology conjecture (8), orthologues tend to be more similar in function than paralogues (9) and are widely used in gene annotation (10, 11).”
PANTHER: Making genome‐scale phylogenetics accessible to all (2021, methodology): “36,55 Users upload a list of genes, and can perform four different analyses.”
g:Profiler—a web server for functional interpretation of gene lists (2016 update) (2016, neutral): “Tools such as Panther (14), FuncAssociate (15) and GOrilla (16) aim to support the analysis of many species, while others such as WebGestalt (17) focus on the convenient mapping of diverse gene identifiers.”
PANTHER version 10: expanded protein families and functions, and analysis tools (2015, methodology): “Users can now select from a number of ‘annotation sets’ when using either the PANTHER overrepresentation tool or the PANTHER enrichment tool (see Mi et al. (9) for more details on these tools).”
Sensing the cilium, digital capture of ciliary data for comparative genomics investigations (2018, methodology): “By manual examination of PANTHER families, we added an additional mouse gene for one of these 301 human genes, as well as two mouse genes most closely related to the remaining human gene where MouseMine did not contain any results, for a total of 310 mouse genes on our list to target for curation ef”
PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements (2016, methodology): “The gene set overrepresentation and enrichment tools compare a user-uploaded gene list to the functional classifications in PANTHER (GO and pathways), to help identify the shared biological functions among genes in the list (8).”