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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.
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.
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.
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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Research works printed but not linked: 17

  1. 10.1093/nar/gkv1194 · DOI · Paper page
  2. 10.1093/bib/bbr042 · DOI
  3. 10.1007/978-1-60761-175-2_7 · DOI
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  6. 10.1073/pnas.0404380101 · DOI
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  8. 10.1038/nprot.2013.092 · DOI
  9. 10.1093/nar/gku1243 · DOI
  10. 10.1093/bioinformatics/btu492 · DOI
  11. 10.1093/nar/gku989 · DOI · Paper page
  12. Gene Ontology Consortium. Expansion of the gene ontology knowledgebase and resources. Nucleic Acid Res. 2017;45. doi:10.1093/nar/gkw1108. · DOI · Paper page
  13. 10.1142/9781848165632_0019 · DOI
  14. 10.1093/nar/gki198 · DOI
  15. 10.1093/nar/gkv1351 · DOI · Paper page
  16. 10.1002/humu.22204 · DOI
  17. 10.1093/bioinformatics/btq028 · DOI

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Metadata

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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CoChat. (2026). Citation check: PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements. https://app.cochat.ai/papers/10.1093/nar/gkw1138
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Mi, H., Huang, X., Muruganujan, A., Tang, H., Mills, C., Kang, D., & Thomas, P. D. (2017). PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements. Nucleic Acids Research. https://doi.org/10.1093/nar/gkw1138