Student or educator? Sign up with your school email and get 6 months of Pro free.
CoChat
Sign Up
Cited by 1,733

The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

Open access
Mi, Huaiyu, Muruganujan, Anushya, Thomas, Paul D.·2012·Nucleic Acids Research
DOI 10.1093/nar/gks1118
Open this paper in CoChat — free account

Abstract

The data and tools in PANTHER-a comprehensive, curated database of protein families, trees, subfamilies and functions available at http://pantherdb.org-have undergone continual, extensive improvement for over a decade. Here, we describe the current PANTHER process as a whole, as well as the website tools for analysis of user-uploaded data. The main goals of PANTHER remain essentially unchanged: the accurate inference (and practical application) of gene and protein function over large sequence databases, using phylogenetic trees to extrapolate from the relatively sparse experimental information from a few model organisms. Yet the focus of PANTHER has continually shifted toward more accurate and detailed representations of evolutionary events in gene family histories. The trees are now designed to represent gene family evolution, including inference of evolutionary events, such as speciation and gene duplication. Subfamilies are still curated and used to define HMMs, but gene ontology functional annotations can now be made at any node in the tree, and are designed to represent gain and loss of function by ancestral genes during evolution. Finally, PANTHER now includes stable database identifiers for inferred ancestral genes, which are used to associate inferred gene attributes with particular genes in the common ancestral genomes of extant species.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1093/nar/gks1118

Cites

6 of 6 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Show all 6 references

Research works printed but not linked: 25

  1. Gene Ontology Consortium, 2012, The Gene Ontology: enhancements for 2011, Nucleic Acids Res., 40, D559, 10.1093/nar/gkr1028 · DOI
  2. Reference Genome Group of the Gene Ontology Consortium, 2009, The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species, PLoS Comput. Biol., 5, e1000431, 10.1371/journal.pcbi.1000431 · DOI
  3. Gaudet, 2011, Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium, Brief Bioinform., 12, 449, 10.1093/bib/bbr042 · DOI
  4. Neely, 2010, A global in vivo Drosophila RNAi screen identifies NOT3 as a conserved regulator of heart function, Cell, 141, 142, 10.1016/j.cell.2010.02.023 · DOI · Paper page
  5. Kang, 2011, HPRT deficiency coordinately dysregulates canonical Wnt and presenilin-1 signaling: a neuro-developmental regulatory role for a housekeeping gene?, PLoS One, 6, 10.1371/annotation/893f09fd-ab24-4119-93f4-44a03a3342f9 · DOI
  6. Verma, 2012, Gene expression profiling and pathway analysis identify the integrin signaling pathway to be altered by IL-1β in human pancreatic cancer cells: role of JNK, Cancer Lett., 320, 86, 10.1016/j.canlet.2012.01.036 · DOI
  7. Thomas, 2003, PANTHER: a library of protein families and subfamilies indexed by function, Genome Res., 13, 2129, 10.1101/gr.772403 · DOI
  8. Mi, 2005, The PANTHER database of protein families, subfamilies, functions and pathways, Nucleic Acids Res., 33, D284, 10.1093/nar/gki078 · DOI · Paper page
  9. Mi, 2007, PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways, Nucleic Acids Res., 35, D247, 10.1093/nar/gkl869 · DOI · Paper page
  10. Mi, 2010, PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium, Nucleic Acids Res., 38, D204, 10.1093/nar/gkp1019 · DOI
  11. Mulder, 2007, InterPro and InterProScan: tools for protein sequence classification and comparison, Methods Mol. Biol., 396, 59, 10.1007/978-1-59745-515-2_5 · DOI · Paper page
  12. Petryszak, 2005, The predictive power of the CluSTr database, Bioinformatics, 21, 3604, 10.1093/bioinformatics/bti542 · DOI
  13. Katoh, 2002, MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform, Nucleic Acids Res., 30, 3059, 10.1093/nar/gkf436 · DOI · Paper page
  14. Thomas, 2010, GIGA: a simple, efficient algorithm for gene tree inference in the genomic age, BMC Bioinform., 11, 312, 10.1186/1471-2105-11-312 · DOI
  15. Fitch, 1970, Distinguishing homologous from analogous proteins, Syst. Zool., 19, 99, 10.2307/2412448 · DOI · Paper page
  16. UniProt Consortium, 2012, Reorganizing the protein space at the Universal Protein Resource (UniProt), Nucleic Acids Res., 40, D71, 10.1093/nar/gkr981 · DOI
  17. Flicek, 2011, Ensembl, Nucleic Acids Res., 39, D800, 10.1093/nar/gkq1064 · DOI · Paper page
  18. Maglott, 2011, Entrez Gene: gene-centered information at NCBI, Nucleic Acids Res., 39, D52, 10.1093/nar/gkq1237 · DOI · Paper page
  19. Funahashi, 2008, CellDesigner 3.5: a versatile modeling tool for biochemical networks, Proc. IEEE, 96, 1254, 10.1109/JPROC.2008.925458 · DOI
  20. Hucka, 2003, The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models, Bioinformatics, 19, 524, 10.1093/bioinformatics/btg015 · DOI · Paper page
  21. van Iersel, 2012, Software support for SBGN maps: SBGN-ML and LibSBGN, Bioinformatics, 28, 2016, 10.1093/bioinformatics/bts270 · DOI
  22. Mi, 2009, PANTHER pathway: an ontology-based pathway database coupled with data analysis tools, Methods Mol. Biol., 563, 123, 10.1007/978-1-60761-175-2_7 · DOI · Paper page
  23. Fink, 2010, Research resource: gonadotropin-releasing hormone receptor-mediated signaling network in LbetaT2 cells: a pathway-based web-accessible knowledgebase, Mol. Endocrinol., 24, 1863, 10.1210/me.2009-0530 · DOI
  24. Kelder, 2012, WikiPathways: building research communities on biological pathways, Nucleic Acids Res., 40, D1301, 10.1093/nar/gkr1074 · DOI · Paper page
  25. Schaefer, 2009, PID: the pathway interaction database, Nucleic Acids Res., 37, D674, 10.1093/nar/gkn653 · DOI · Paper page

Cited by

Metadata

Authors
Mi, H., Muruganujan, A., & Thomas, P. D.
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2012-11-26
Volume
41
Issue
D1
Pages
D377-D386
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gks1118
OpenAlex
W2022472106
Cited by
1,733
References
6
FWCI
48.68
Type
journal article
Language
en
Open access
gold
Licence
creativecommons.org/licenses/by-nc/3.0 (vor, 1408 d)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.