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Title: PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium

Abstract

Protein Analysis Through Evolutionary Relationships (PANTHER) is a comprehensive software system for inferring the functions of genes based on their evolutionary relationships. Phylogenetic trees of gene families form the basis for PANTHER and these trees are annotated with ontology terms describing the evolution of gene function from ancestral to modern day genes. One of the main applications of PANTHER is in accurate prediction of the functions of uncharacterized genes, based on their evolutionary relationships to genes with functions known from experiment. The PANTHER website, freely available at http://www.pantherdb .org, also includes software tools for analyzing genomic data relative to known and inferred gene functions. Since 2007, there have been several new developments to PANTHER: (i) improved phylogenetic trees, explicitly representing speciation and gene duplication events, (ii) identification of gene orthologs, including least diverged orthologs (best one-to-one pairs), (iii) coverage of more genomes (48 genomes, up to 87% of genes in each genome; see http://www.pantherdb.org/ panther/summaryStats.jsp), (iv) improved support for alternative database identifiers for genes, proteins and microarray probes and (v) adoption of the SBGN standard for display of biological pathways. In addition, PANTHER trees are being annotated with gene function as part of the Gene Ontology Reference Genome project, resultingmore » in an increasing number of curated functional annotations.« less

Authors:
 [1];  [1];  [1];  [2];  [3];  [1]
+ Show Author Affiliations
  1. SRI International, Menlo Park, CA (United States). Evolutionary Systems Biology Group
  2. Northwestern Univ., Evanston, IL (United States). dictyBase
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Berkeley Bioinformatics and Open-source Projects (BBOP)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
OSTI Identifier:
1625458
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Volume: 38; Journal Issue: suppl_1; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biochemistry & Molecular Biology

Citation Formats

Mi, Huaiyu, Dong, Qing, Muruganujan, Anushya, Gaudet, Pascale, Lewis, Suzanna, and Thomas, Paul D. PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. United States: N. p., 2009. Web. doi:10.1093/nar/gkp1019.
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Mi, Huaiyu, Dong, Qing, Muruganujan, Anushya, Gaudet, Pascale, Lewis, Suzanna, & Thomas, Paul D. PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. United States. https://doi.org/10.1093/nar/gkp1019
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Mi, Huaiyu, Dong, Qing, Muruganujan, Anushya, Gaudet, Pascale, Lewis, Suzanna, and Thomas, Paul D. Wed . "PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium". United States. https://doi.org/10.1093/nar/gkp1019. https://www.osti.gov/servlets/purl/1625458.
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@article{osti_1625458,
title = {PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium},
author = {Mi, Huaiyu and Dong, Qing and Muruganujan, Anushya and Gaudet, Pascale and Lewis, Suzanna and Thomas, Paul D.},
abstractNote = {Protein Analysis Through Evolutionary Relationships (PANTHER) is a comprehensive software system for inferring the functions of genes based on their evolutionary relationships. Phylogenetic trees of gene families form the basis for PANTHER and these trees are annotated with ontology terms describing the evolution of gene function from ancestral to modern day genes. One of the main applications of PANTHER is in accurate prediction of the functions of uncharacterized genes, based on their evolutionary relationships to genes with functions known from experiment. The PANTHER website, freely available at http://www.pantherdb .org, also includes software tools for analyzing genomic data relative to known and inferred gene functions. Since 2007, there have been several new developments to PANTHER: (i) improved phylogenetic trees, explicitly representing speciation and gene duplication events, (ii) identification of gene orthologs, including least diverged orthologs (best one-to-one pairs), (iii) coverage of more genomes (48 genomes, up to 87% of genes in each genome; see http://www.pantherdb.org/ panther/summaryStats.jsp), (iv) improved support for alternative database identifiers for genes, proteins and microarray probes and (v) adoption of the SBGN standard for display of biological pathways. In addition, PANTHER trees are being annotated with gene function as part of the Gene Ontology Reference Genome project, resulting in an increasing number of curated functional annotations.},
doi = {10.1093/nar/gkp1019},
journal = {Nucleic Acids Research},
number = suppl_1,
volume = 38,
place = {United States},
year = {Wed Dec 16 00:00:00 EST 2009},
month = {Wed Dec 16 00:00:00 EST 2009}
}
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    An integrated genome-wide multi-omics analysis of gene expression dynamics in the preimplantation mouse embryo
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    Genome-wide association analysis of coffee drinking suggests association with CYP1A1/CYP1A2 and NRCAM
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    Ribosome profiling of selenoproteins in vivo reveals consequences of pathogenic Secisbp2 missense mutations
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    QuantumClone: clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction
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    Interference between arsenic-induced toxicity and hypoxia: Interference between hypoxia and arsenic toxicity
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    Glucagon-like peptide-1 receptor and sarcoglycan delta genetic variants can affect cardiovascular risk in chronic kidney disease patients under hemodialysis
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    Genome structure predicts modular transcriptome responses to genetic and environmental conditions
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    Herpesvirus deconjugases inhibit the IFN response by promoting TRIM25 autoubiquitination and functional inactivation of the RIG-I signalosome
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    Automated Isoform Diversity Detector (AIDD): a pipeline for investigating transcriptome diversity of RNA-seq data
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    Chromatin changes in Anopheles gambiae induced by Plasmodium falciparum infection
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    Revealing Mammalian Evolutionary Relationships by Comparative Analysis of Gene Clusters
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    Copy number variation in schizophrenia in Sweden
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    • E., Bergen, S.; A., Kähler,; E., Magnusson, P. K.
    • The University of North Carolina at Chapel Hill University Libraries
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    Phylotranscriptomic analysis uncovers a wealth of tissue inhibitor of metalloproteinases variants in echinoderms
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    Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants
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    Genomewide Analyses Define Different Modes of Transcriptional Regulation by Peroxisome Proliferator-Activated Receptor-β/δ (PPARβ/δ)
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    Horizontal Transfer of a Subtilisin Gene from Plants into an Ancestor of the Plant Pathogenic Fungal Genus Colletotrichum
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    APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins
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    Dual Lineage-Specific Expression of Sox17 During Mouse Embryogenesis: Lineage-Specific Expression of Sox17
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    A novel P66S mutation in exon 3 of the SOD1 gene with early onset and rapid progression
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    Decreased Protein Kinase C-β Type II Associated with the Prominent Endotoxin Exhaustion in the Macrophage of FcGRIIb−/− Lupus Prone Mice is Revealed by Phosphoproteomic Analysis
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    Non-Coding Transcriptome Maps across Twenty Tissues of the Korean Black Chicken, Yeonsan Ogye
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    Survey of human chromosome 21 gene expression effects on early development in Danio rerio
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    Genetic architectures of psychiatric disorders: the emerging picture and its implications
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    • J., Daly, Mark; Michael, O'Donovan,; F., Sullivan, Patrick
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    Genome structure predicts modular transcriptome responses to genetic and environmental conditions
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    CardioGenBase: A Literature Based Multi-Omics Database for Major Cardiovascular Diseases
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    Finding the missing honey bee genes: lessons learned from a genome upgrade
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    DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes
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    Tissue damage in organic rainbow trout muscle investigated by proteomics and bioinformatics
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    The endogenous molecular clock orchestrates the temporal separation of substrate metabolism in skeletal muscle
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    Annexin A3 as a Potential Target for Immunotherapy of Liver Cancer Stem-Like Cells: ANXA3 for Cancer Stem-Like Cell Immunotherapy
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    Characterization of an M28 metalloprotease family member residing in the yeast vacuole
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    • Hecht, Karen A.; Wytiaz, Victoria A.; Ast, Tslil
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    Genome-wide strategies identify downstream target genes of chick connective tissue-associated transcription factors
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    Effect of ovarian cancer ascites on SKOV-3 cells proteome: new proteins associated with aggressive phenotype in epithelial ovarian cancer
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    • Toledo-Leyva, Alfredo; Villegas-Pineda, Julio César; Encarnación-Guevara, Sergio
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    Prolonged Waking and Recovery Sleep Affect the Serum MicroRNA Expression Profile in Humans
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    • Weigend, Susanne; Holst, Sebastian; Meier, Josefine
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    Proteomic analysis of human substantia nigra identifies novel candidates involved in Parkinson's disease pathogenesis
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    Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome
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    Human Hepatocyte Nuclear Factor 4-α encodes isoforms with distinct transcriptional functions
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    Mouse Genome Database: From sequence to phenotypes and disease models
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    Analysis of cyclin E co‐expression genes reveals nuclear transcription factor Y subunit alpha is an oncogene in gastric cancer
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    A dataset for assessing temporal changes in gene expression during the aging process of adult Drosophila melanogaster
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    SNVDis: A Proteome-wide Analysis Service for Evaluating nsSNVs in Protein Functional Sites and Pathways
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    Porcine Esophageal Submucosal Gland Culture Model Shows Capacity for Proliferation and Differentiation
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    Proteomic profiling of ATM kinase proficient and deficient cell lines upon blockage of proteasome activity
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    m6A enhances the phase separation potential of mRNA
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    Proteotranscriptomics Reveal Signaling Networks in the Ovarian Cancer Microenvironment
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    The dilemma of bacterial expansins evolution. The unusual case of Streptomyces acidiscabies and Kutzneria sp. 744
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    Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium
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    T2D@ZJU: a knowledgebase integrating heterogeneous connections associated with type 2 diabetes mellitus
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    iPathCons and iPathDB: an improved insect pathway construction tool and the database
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    DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes
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    GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations
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    Emergence and Evolution of Hominidae-Specific Coding and Noncoding Genomic Sequences
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    Advances and Applications in the Quest for Orthologs
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    The Gene Ontology in 2010: extensions and refinements
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    SPOT: a web-based tool for using biological databases to prioritize SNPs after a genome-wide association study
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    The Protein Ontology: a structured representation of protein forms and complexes
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    MOPED: Model Organism Protein Expression Database
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    HMMER web server: interactive sequence similarity searching
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    ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework
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    OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs
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    PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees
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    GFam: a platform for automatic annotation of gene families
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    TSGene: a web resource for tumor suppressor genes
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    • Zhao, Min; Sun, Jingchun; Zhao, Zhongming
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    The InterPro protein families database: the classification resource after 15 years
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    FlyRNAi.org—the database of the Drosophila RNAi screening center and transgenic RNAi project: 2017 update
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    Human DDX21 binds and unwinds RNA guanine quadruplexes
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    Phylotranscriptomic analysis uncovers a wealth of tissue inhibitor of metalloproteinases variants in echinoderms
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    APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins
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    An integrated genome-wide multi-omics analysis of gene expression dynamics in the preimplantation mouse embryo
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    Systematic Dissection of the Evolutionarily Conserved WetA Developmental Regulator across a Genus of Filamentous Fungi
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    Reconciliation of Gene and Species Trees
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    Biomechanical Rigidity and Quantitative Proteomics Analysis of Segmental Regions of the Trabecular Meshwork at Physiologic and Elevated Pressures
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    Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data
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    Changes in predicted protein disorder tendency may contribute to disease risk
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    Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping
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    Exosomes secreted by human cells transport largely mRNA fragments that are enriched in the 3′-untranslated regions
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    Tight regulation of wingless-type signaling in the articular cartilage - subchondral bone biomechanical unit: transcriptomics in Frzb-knockout mice
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    H3K4me3 inversely correlates with DNA methylation at a large class of non-CpG-island-containing start sites
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    Chromatin changes in Anopheles gambiae induced by Plasmodium falciparum infection
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    Using Biological Pathway Data with Paxtools
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    MicroRNA Expression and Regulation in Human, Chimpanzee, and Macaque Brains
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    Massive-Scale RNA-Seq Analysis of Non Ribosomal Transcriptome in Human Trisomy 21
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    Genome-Wide Signatures of ‘Rearrangement Hotspots’ within Segmental Duplications in Humans
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    Gene-Based Analysis of Regionally Enriched Cortical Genes in GWAS Data Sets of Cognitive Traits and Psychiatric Disorders
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    Global Identification of Prokaryotic Glycoproteins Based on an Escherichia coli Proteome Microarray
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    Global Effect of Inauhzin on Human p53-Responsive Transcriptome
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    Horizontal Transfer of a Subtilisin Gene from Plants into an Ancestor of the Plant Pathogenic Fungal Genus Colletotrichum
    journal, March 2013

    • Armijos Jaramillo, Vinicio Danilo; Vargas, Walter Alberto; Sukno, Serenella Ana
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    LABEL: Fast and Accurate Lineage Assignment with Assessment of H5N1 and H9N2 Influenza A Hemagglutinins
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    Genome-Wide Microarray Expression and Genomic Alterations by Array-CGH Analysis in Neuroblastoma Stem-Like Cells
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    CardioGenBase: A Literature Based Multi-Omics Database for Major Cardiovascular Diseases
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    WetA bridges cellular and chemical development in Aspergillus flavus
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    Phosphoproteomic Analyses Reveal Signaling Pathways That Facilitate Lytic Gammaherpesvirus Replication
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    Genome-Wide Divergence in the West-African Malaria Vector Anopheles melas
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    Bioinformatics-based identification of potential microRNA biomarkers in frequent and non-frequent exacerbators of COPD
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    • Liu, Xiao; Qu, Jingge; Xue, Weixiao
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    Integrated Analysis of Transcriptomic and Proteomic Data
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    Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome
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    Differential Gene Expression in Articular Cartilage and Subchondral Bone of Neonatal and Adult Horses
    journal, September 2019

    Identification of Key Candidate Genes and Pathways in Colorectal Cancer by Integrated Bioinformatical Analysis
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    • Guo, Yongchen; Bao, Yonghua; Ma, Ming
    • International Journal of Molecular Sciences, Vol. 18, Issue 4
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    Non-Coding Transcriptome Maps across Twenty Tissues of the Korean Black Chicken, Yeonsan Ogye
    journal, August 2018

    • Hong, Hyosun; Chai, Han-Ha; Nam, Kyoungwoo
    • International Journal of Molecular Sciences, Vol. 19, Issue 8
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    Circular RNA Signature in Hepatocellular Carcinoma
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    • Qiu, Lipeng; Wang, Tao; Ge, Qi
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    Dual-platform affinity proteomics identifies links between the recurrence of ovarian carcinoma and proteins released into the tumor microenvironment
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    • Finkernagel, Florian; Reinartz, Silke; Schuldner, Maximiliane
    • Theranostics, Vol. 9, Issue 22
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    We are not so special
    journal, July 2018

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