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

Huaiyu Mi, Xiaosong Huang, Anushya Muruganujan, Haiming Tang, Caitlin Mills, Diane Kang, Paul D. Thomas
2016 Nucleic Acids Research  
For human genes (as well as a few other organisms), PAN-THER now also supports enrichment analysis using pathway classifications from the Reactome resource.  ...  PANTHER software tools allow users to classify new protein sequences, and to analyze gene lists obtained from large-scale genomics experiments.  ...  The authors would also like to acknowledge the Reactome developers for their excellent work on the resource, and Robin Haw for valuable input on integrating the Reactome data. FUNDING  ... 
doi:10.1093/nar/gkw1138 pmid:27899595 pmcid:PMC5210595 fatcat:atj6sbwxqvbpnkrbxytom7u3gq

PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API

Huaiyu Mi, Dustin Ebert, Anushya Muruganujan, Caitlin Mills, Laurent-Philippe Albou, Tremayne Mushayamaha, Paul D Thomas
2020 Nucleic Acids Research  
We have also expanded the available services for programmatic access to PANTHER tools and data via application programming interfaces (APIs).  ...  We have added human enhancer-gene links that associate non-coding regions with the annotated human genes in PANTHER.  ...  ACKNOWLEDGEMENTS The authors want to thank the GO Phylogenetic Annotation curators for QA of the phylogenetic trees and family members: Marc Feuermann, Michael Kesling, Pascale Gaudet, Karen Christie,  ... 
doi:10.1093/nar/gkaa1106 pmid:33290554 pmcid:PMC7778891 fatcat:ud5tcejh2fgifjkxjwoz7rc6aq

A human functional protein interaction network and its application to cancer data analysis

Guanming Wu, Xin Feng, Lincoln Stein
2010 Genome Biology  
[23] Panther [60] KEGG [63] TRED [64] NCI-BioCarta [62] NCI-Nature [62] CellMap [61] Reactome [23] Panther [60] KEGG [63] TRED [64] NCI-BioCarta [62] NCI-Nature [62] CellMap [61] Na Data sources for annotated  ...  domain interaction, Gene Ontology (GO) annotations and text-mined protein interactions, which cover close to 50% of the human proteome.  ...  The data and data model from the Reactome project form the basis of this work.  ... 
doi:10.1186/gb-2010-11-5-r53 pmid:20482850 pmcid:PMC2898064 fatcat:vntehsevq5gcrfppuzcikesvde

HPD: an online integrated human pathway database enabling systems biology studies

Sudhir R Chowbina, Xiaogang Wu, Fan Zhang, Peter M Li, Ragini Pandey, Harini N Kasamsetty, Jake Y Chen
2009 BMC Bioinformatics  
This pathway tool enables users to 1) search for human pathways from different resources by simply entering genes/proteins involved in pathways or words appearing in pathway names, 2) analyze pathway-protein  ...  Integration of pathway data at syntactic, semantic, and schematic levels was based on a unified pathway data model and data warehousing-based integration techniques.  ...  We thank Stephanie Burks and Joseph Rinkovsky from the University Information Technology and Services (UITS) at Indiana University for providing generous support in Oracle 10 g database administration  ... 
doi:10.1186/1471-2105-10-s11-s5 pmid:19811689 pmcid:PMC3226194 fatcat:36hdxinevfd6rojoziqdx4fkue

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

Huaiyu Mi, Anushya Muruganujan, Paul D. Thomas
2012 Nucleic Acids Research  
Here, we describe the current PANTHER process as a whole, as well as the website tools for analysis of user-uploaded data.  ...  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  ...  ACKNOWLEDGEMENTS We thank John Casagrande for PANTHER database extensions and data loader enhancements in version 8. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gks1118 pmid:23193289 pmcid:PMC3531194 fatcat:penzalro4zfajejys6bs2cas5u

The Gene Ontology of eukaryotic cilia and flagella

Paola Roncaglia, Teunis J. P. van Dam, Karen R. Christie, Lora Nacheva, Grischa Toedt, Martijn A. Huynen, Rachael P. Huntley, Toby J. Gibson, Jane Lomax
2017 Cilia  
These improvements in ontology and protein annotation will benefit all users of GO enrichment analysis tools, as well as the ciliary research community, in areas ranging from microscopy image annotation  ...  Methods: Members of the SYSCILIA and Gene Ontology Consortia suggested additions and changes to GO, to reflect new knowledge in the field.  ...  ; Dragana Mitic Potkrajac and Ana Stelkic (CCNET) for contributing to gene annotation efforts.  ... 
doi:10.1186/s13630-017-0054-8 pmid:29177046 pmcid:PMC5688719 fatcat:ohsarelpmnf5tiaz27ickkzizm

Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome

Marija Milacic, Robin Haw, Karen Rothfels, Guanming Wu, David Croft, Henning Hermjakob, Peter D'Eustachio, Lincoln Stein
2012 Cancers  
The curation of pathways associated with cancer, coupled with our efforts to create other disease-specific pathways, will interoperate with our existing pathway and network analysis tools.  ...  Recent extensions of our data model accommodate the annotation of cancer and other disease processes.  ...  Acknowledgments The data, data model, and data analysis tools described in this article are the product of the collaborative work of curators and software developers at the Ontario Institute for Cancer  ... 
doi:10.3390/cancers4041180 pmid:24213504 pmcid:PMC3712731 fatcat:yuq7zjs3z5edxngpwzncfa7jaq

Protein Ontology (PRO): enhancing and scaling up the representation of protein entities

Darren A. Natale, Cecilia N. Arighi, Judith A. Blake, Jonathan Bona, Chuming Chen, Sheng-Chih Chen, Karen R. Christie, Julie Cowart, Peter D'Eustachio, Alexander D. Diehl, Harold J. Drabkin, William D. Duncan (+10 others)
2016 Nucleic Acids Research  
; proteins produced from a given gene; and proteincontaining complexes.  ...  We illustrate its use in facilitating an alignment between PRO and Reactome protein entities.  ...  ACKNOWLEDGEMENTS The authors thank the collaborating groups mentioned in this manuscript for their contribution to PRO and/or usage of PRO. Author contributions are as follows: Writing  ... 
doi:10.1093/nar/gkw1075 pmid:27899649 pmcid:PMC5210558 fatcat:xwzphiew4rcuzjmvb55fw4wf5i

Gramene 2021: harnessing the power of comparative genomics and pathways for plant research

Marcela K Tello-Ruiz, Sushma Naithani, Parul Gupta, Andrew Olson, Sharon Wei, Justin Preece, Yinping Jiao, Bo Wang, Kapeel Chougule, Priyanka Garg, Justin Elser, Sunita Kumari (+17 others)
2020 Nucleic Acids Research  
Gramene integrates ontology-based protein structure–function annotation; information on genetic, epigenetic, expression, and phenotypic diversity; and gene functional annotations extracted from plant-focused  ...  The Reactome platform facilitates comparison between reference and projected pathways, gene expression analyses and overlays of genegene interactions.  ...  Marco and David Micklos (MaizeCode Project) for jointly running the maize gene structural annotation jamborees.  ... 
doi:10.1093/nar/gkaa979 pmid:33170273 fatcat:atundz637bfalivwtye3vb3twe

Shared Biological Pathways Between Alzheimer's Disease and Ischemic Stroke

Pan Cui, Xiaofeng Ma, He Li, Wenjing Lang, Junwei Hao
2018 Frontiers in Neuroscience  
well-studied databases, including GO, KEGG, PANTHER, Reactome, and Wikipathways.  ...  We took advantage of large-scale GWAS summary data of AD (17,008 AD cases and 37,154 controls) and IS (10,307 cases and 19,326 controls) to conduct pathway analyses using genetic pathways from multiple  ...  ACKNOWLEDGMENTS We thank the International Genomics of Alzheimer's Project (IGAP) and METASTROKE collaboration for providing summary results data for these analyses.  ... 
doi:10.3389/fnins.2018.00605 pmid:30245614 pmcid:PMC6137293 fatcat:s6wtkmski5fktg5mxmksfdz4yq

Biomarkers for tissue engineering of the tendon-bone interface

Lara A. Kuntz, Leone Rossetti, Elena Kunold, Andreas Schmitt, Ruediger von Eisenhart-Rothe, Andreas R. Bausch, Rainer H. Burgkart, Florence Ruggiero
2018 PLoS ONE  
Integrative analysis of transcriptome and proteome data identified ten enthesis biomarkers and six tendon biomarkers.  ...  The observed gene expression characteristics and differentiation markers shed light into the nature of the cells present at the enthesis.  ...  Acknowledgments Research was supported by the International Graduate School of Science and Engineering. The authors acknowledge the continuous support of the German Research Foundation (DFG).  ... 
doi:10.1371/journal.pone.0189668 pmid:29298298 pmcid:PMC5751986 fatcat:kf5vmc6xmvdqroltkccwmfowom

Shared Gene Expression Between Multiple Sclerosis and Ischemic Stroke

He Li, Lin Chen, Xiaofeng Ma, Pan Cui, Wenjing Lang, Junwei Hao
2019 Frontiers in Genetics  
After identifying significant gene sets individually of MS and IS, we performed pathway-based analysis in four biological pathway databases (KEGG, PANTHER, REACTOME, and WikiPathways) and GO categories  ...  We discovered that there were 9 shared pathways between MS and IS in KEGG, 2 in PANTHER, 14 in REACTOME, 1 in WikiPathways, and 194 in GO annotations (p < 0.05).  ...  T., and Thomas, P. D. (2016). PANTHER version 10: expanded protein families and functions, and analysis tools.  ... 
doi:10.3389/fgene.2018.00598 pmid:30809253 pmcid:PMC6379658 fatcat:mgp332tfxvfojohyex4vlekrpe

Reactome: a knowledge base of biologic pathways and processes

Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Geeta Joshi-Tope, Gopal Gopinath, David Croft, Bernard de Bono, Marc Gillespie, Bijay Jassal, Suzanna Lewis, Lisa Matthews, Guanming Wu (+2 others)
2007 Genome Biology  
Reactome Reactome, an online curated resource for human pathway data, can be used to infer equivalent reactions in non-human species and as a tool to aid in the interpretation of microarrays and other  ...  Finally, we describe the use of Reactome both as a learning resource and as a computational tool to aid in the interpretation of microarrays and similar large-scale datasets.  ...  Acknowledgements The development of Reactome is supported by a grant from the US National Institutes of Health (R01 HG002639), a grant from the European Reactions colored according to the most distant  ... 
doi:10.1186/gb-2007-8-3-r39 pmid:17367534 pmcid:PMC1868929 fatcat:pec5fg3igbgybpklqebttp4bqy

Framework for a protein ontology

Darren A. Natale, Cecilia N. Arighi, Winona Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith, Cathy H. Wu
2006 Proceedings of the 1st international workshop on Text mining in bioinformatics - TMBIO '06  
Biomedical ontologies are emerging as critical tools in genomic and proteomic research, where complex data in disparate resources need to be integrated.  ...  We have designed the PRotein Ontology (PRO) to facilitate protein annotation and to guide new experiments.  ...  Later versions will be expanded to additional proteins from these and other pathways. Figure 5 illustrates the PRO structure for the Smad2 protein.  ... 
doi:10.1145/1183535.1183544 fatcat:5xofoicamzboxp3cjmnfziwmqa

Framework for a Protein Ontology

Darren A Natale, Cecilia N Arighi, Winona C Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith, Cathy H Wu
2007 BMC Bioinformatics  
Biomedical ontologies are emerging as critical tools in genomic and proteomic research, where complex data in disparate resources need to be integrated.  ...  We have designed the PRotein Ontology (PRO) to facilitate protein annotation and to guide new experiments.  ...  Later versions will be expanded to additional proteins from these and other pathways. Figure 5 illustrates the PRO structure for the Smad2 protein.  ... 
doi:10.1186/1471-2105-8-s9-s1 pmid:18047702 pmcid:PMC2217659 fatcat:z7k56eb7rvcntbqzq2fadogcsq
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