PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements

Mi, Huaiyu, Huang, Xiaosong, Muruganujan, Anushya, Tang, Haiming, Mills, Caitlin, Kang, Diane, Thomas, Paul D.·2017·Nucleic Acids Research

DOI 10.1093/nar/gkw1138PMC PMC5210595

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Figure 1. Reactome pathways in the PANTHER gene list analysis tool. Users can select Reactome pathways from a drop-down list of annotation sets. They can also upload a custom reference list for calculating overrepresentation by clicking on the ‘Change’ button. The Reactome pathways are accessible to both statistical test types in PANTHER: the overrepresentation tool (shown here) that takes a user-uploaded gene list as input, and the enrichment tool (not shown), that takes a user-uploaded list of genes, each of which is associated with a value, such as log-fold-change in expression or association P-value.CC BY-NC · PubMed Central

Figure 2. Hierarchical view of GO (molecular function) in gene list analysis result page. Each block of related function classes (the first block starts with AMP-activated protein kinase activity, the second with acid-sensing ion channel activity) is arranged with the most specific class at the top, with less specific classes indented below it.CC BY-NC · PubMed Central

Figure 3. Tree Viewer, showing the tree panel on the left, and multiple sequence alignment panel on the right with the ‘Evolutionary History’ view selected. This view shows in red text the amino acids that have changed in the tree branch immediately leading to each sequence. (A) The standard ‘phylogenetic view’ of the tree, showing only the sequences of the leaves (extant genes) of the tree. (B) The new ‘hierarchical view’ of the tree, showing the sequences of both internal nodes (inferred ancestral sequences) and leaves.CC BY-NC · PubMed Central

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10.1093/nar/gkv1194 · DOI · Paper page
10.1093/bib/bbr042 · DOI
10.1007/978-1-60761-175-2_7 · DOI
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Gene Ontology Consortium. Expansion of the gene ontology knowledgebase and resources. Nucleic Acid Res. 2017;45. doi:10.1093/nar/gkw1108. · DOI · Paper page
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10.1093/nar/gkv1351 · DOI · Paper page
10.1002/humu.22204 · DOI
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“8, Laboratory of Human Retrovirology and Immunoinformatics, Frederick, MD, USA) [43], Gene Set Enrichment Analysis (GSEA) [44], gProfileR [45] and The PANTHER database (Protein ANalysis THrough Evolutionary Relationships) [46] were used to annotate the functions of the differentially expressed genes.”
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OUP accepted manuscript
(2020) · Database · doi:10.1093/database/baaa086 · Cited by 5

Authors: Mi, H., Huang, X., Muruganujan, A., Tang, H., Mills, C., Kang, D., & Thomas, P. D.
Venue: Nucleic Acids Research
Publisher: Oxford University Press (OUP)
Published: 2016-11-29
Volume: 45
Issue: D1
Pages: D183-D189
ISSN: 0305-1048
1362-4962
DOI: 10.1093/nar/gkw1138
PMC: PMC5210595
Cited by: 1,874
References: 0
Language: en
Licence: creativecommons.org/licenses/by-nc/4.0/ (vor)

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PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements

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