Literature DB >> 23547033

PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways.

Jake Y Fried1, Martijn P van Iersel, Mirit I Aladjem, Kurt W Kohn, Augustin Luna.   

Abstract

PURPOSE: The PathVisio-Faceted Search plugin helps users explore and understand complex pathways by overlaying experimental data and data from webservices, such as Ensembl BioMart, onto diagrams drawn using formalized notations in PathVisio. The plugin then provides a filtering mechanism, known as a faceted search, to find and highlight diagram nodes (e.g. genes and proteins) of interest based on imported data. The tool additionally provides a flexible scripting mechanism to handle complex queries. AVAILABILITY: The PathVisio-Faceted Search plugin is compatible with PathVisio 3.0 and above. PathVisio is compatible with Windows, Mac OS X and Linux. The plugin, documentation, example diagrams and Groovy scripts are available at http://PathVisio.org/wiki/PathVisioFacetedSearchHelp. The plugin is free, open-source and licensed by the Apache 2.0 License.

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Year:  2013        PMID： 23547033      PMCID： PMC3661049          DOI： 10.1093/bioinformatics/btt146

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  10 in total

1.  GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways.

Authors:  Kam D Dahlquist; Nathan Salomonis; Karen Vranizan; Steven C Lawlor; Bruce R Conklin
Journal:  Nat Genet       Date:  2002-05       Impact factor: 38.330

2.  The Systems Biology Graphical Notation.

Authors:  Nicolas Le Novère; Michael Hucka; Huaiyu Mi; Stuart Moodie; Falk Schreiber; Anatoly Sorokin; Emek Demir; Katja Wegner; Mirit I Aladjem; Sarala M Wimalaratne; Frank T Bergman; Ralph Gauges; Peter Ghazal; Hideya Kawaji; Lu Li; Yukiko Matsuoka; Alice Villéger; Sarah E Boyd; Laurence Calzone; Melanie Courtot; Ugur Dogrusoz; Tom C Freeman; Akira Funahashi; Samik Ghosh; Akiya Jouraku; Sohyoung Kim; Fedor Kolpakov; Augustin Luna; Sven Sahle; Esther Schmidt; Steven Watterson; Guanming Wu; Igor Goryanin; Douglas B Kell; Chris Sander; Herbert Sauro; Jacky L Snoep; Kurt Kohn; Hiroaki Kitano
Journal:  Nat Biotechnol       Date:  2009-08-07       Impact factor: 54.908

3.  CySBGN: a Cytoscape plug-in to integrate SBGN maps.

Authors:  Emanuel Gonçalves; Martijn van Iersel; Julio Saez-Rodriguez
Journal:  BMC Bioinformatics       Date:  2013-01-16       Impact factor: 3.169

4.  Cytoscape 2.8: new features for data integration and network visualization.

Authors:  Michael E Smoot; Keiichiro Ono; Johannes Ruscheinski; Peng-Liang Wang; Trey Ideker
Journal:  Bioinformatics       Date:  2010-12-12       Impact factor: 6.937

5.  A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method.

Authors:  Augustin Luna; Evrim I Karac; Margot Sunshine; Lucas Chang; Ruth Nussinov; Mirit I Aladjem; Kurt W Kohn
Journal:  BMC Bioinformatics       Date:  2011-05-17       Impact factor: 3.169

6.  The BioPAX community standard for pathway data sharing.

Authors:  Emek Demir; Michael P Cary; Suzanne Paley; Ken Fukuda; Christian Lemer; Imre Vastrik; Guanming Wu; Peter D'Eustachio; Carl Schaefer; Joanne Luciano; Frank Schacherer; Irma Martinez-Flores; Zhenjun Hu; Veronica Jimenez-Jacinto; Geeta Joshi-Tope; Kumaran Kandasamy; Alejandra C Lopez-Fuentes; Huaiyu Mi; Elgar Pichler; Igor Rodchenkov; Andrea Splendiani; Sasha Tkachev; Jeremy Zucker; Gopal Gopinath; Harsha Rajasimha; Ranjani Ramakrishnan; Imran Shah; Mustafa Syed; Nadia Anwar; Ozgün Babur; Michael Blinov; Erik Brauner; Dan Corwin; Sylva Donaldson; Frank Gibbons; Robert Goldberg; Peter Hornbeck; Augustin Luna; Peter Murray-Rust; Eric Neumann; Oliver Ruebenacker; Oliver Reubenacker; Matthias Samwald; Martijn van Iersel; Sarala Wimalaratne; Keith Allen; Burk Braun; Michelle Whirl-Carrillo; Kei-Hoi Cheung; Kam Dahlquist; Andrew Finney; Marc Gillespie; Elizabeth Glass; Li Gong; Robin Haw; Michael Honig; Olivier Hubaut; David Kane; Shiva Krupa; Martina Kutmon; Julie Leonard; Debbie Marks; David Merberg; Victoria Petri; Alex Pico; Dean Ravenscroft; Liya Ren; Nigam Shah; Margot Sunshine; Rebecca Tang; Ryan Whaley; Stan Letovksy; Kenneth H Buetow; Andrey Rzhetsky; Vincent Schachter; Bruno S Sobral; Ugur Dogrusoz; Shannon McWeeney; Mirit Aladjem; Ewan Birney; Julio Collado-Vides; Susumu Goto; Michael Hucka; Nicolas Le Novère; Natalia Maltsev; Akhilesh Pandey; Paul Thomas; Edgar Wingender; Peter D Karp; Chris Sander; Gary D Bader
Journal:  Nat Biotechnol       Date:  2010-09-09       Impact factor: 54.908

7.  BioMart Central Portal: an open database network for the biological community.

Authors:  Jonathan M Guberman; J Ai; O Arnaiz; Joachim Baran; Andrew Blake; Richard Baldock; Claude Chelala; David Croft; Anthony Cros; Rosalind J Cutts; A Di Génova; Simon Forbes; T Fujisawa; E Gadaleta; D M Goodstein; Gunes Gundem; Bernard Haggarty; Syed Haider; Matthew Hall; Todd Harris; Robin Haw; S Hu; Simon Hubbard; Jack Hsu; Vivek Iyer; Philip Jones; Toshiaki Katayama; R Kinsella; Lei Kong; Daniel Lawson; Yong Liang; Nuria Lopez-Bigas; J Luo; Michael Lush; Jeremy Mason; Francois Moreews; Nelson Ndegwa; Darren Oakley; Christian Perez-Llamas; Michael Primig; Elena Rivkin; S Rosanoff; Rebecca Shepherd; Reinhard Simon; B Skarnes; Damian Smedley; Linda Sperling; William Spooner; Peter Stevenson; Kevin Stone; J Teague; Jun Wang; Jianxin Wang; Brett Whitty; D T Wong; Marie Wong-Erasmus; L Yao; Ken Youens-Clark; Christina Yung; Junjun Zhang; Arek Kasprzyk
Journal:  Database (Oxford)       Date:  2011-09-18       Impact factor: 3.451

8.  The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services.

Authors:  Martijn P van Iersel; Alexander R Pico; Thomas Kelder; Jianjiong Gao; Isaac Ho; Kristina Hanspers; Bruce R Conklin; Chris T Evelo
Journal:  BMC Bioinformatics       Date:  2010-01-04       Impact factor: 3.169

9.  Presenting and exploring biological pathways with PathVisio.

Authors:  Martijn P van Iersel; Thomas Kelder; Alexander R Pico; Kristina Hanspers; Susan Coort; Bruce R Conklin; Chris Evelo
Journal:  BMC Bioinformatics       Date:  2008-09-25       Impact factor: 3.169

10.  WikiPathways: pathway editing for the people.

Authors:  Alexander R Pico; Thomas Kelder; Martijn P van Iersel; Kristina Hanspers; Bruce R Conklin; Chris Evelo
Journal:  PLoS Biol       Date:  2008-07-22       Impact factor: 8.029
  10 in total
  3 in total

1.  Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment.

Authors:  Anwesha Bohler; Lars M T Eijssen; Martijn P van Iersel; Christ Leemans; Egon L Willighagen; Martina Kutmon; Magali Jaillard; Chris T Evelo
Journal:  BMC Bioinformatics       Date:  2015-08-23       Impact factor: 3.169

2.  PathVisio 3: an extendable pathway analysis toolbox.

Authors:  Martina Kutmon; Martijn P van Iersel; Anwesha Bohler; Thomas Kelder; Nuno Nunes; Alexander R Pico; Chris T Evelo
Journal:  PLoS Comput Biol       Date:  2015-02-23       Impact factor: 4.475

3.  Identification of Potential Anticancer Activities of Novel Ganoderma lucidum Extracts Using Gene Expression and Pathway Network Analysis.

Authors:  Chi H J Kao; Karen S Bishop; Yuanye Xu; Dug Yeo Han; Pamela M Murray; Gareth J Marlow; Lynnette R Ferguson
Journal:  Genomics Insights       Date:  2016-02-16
  3 in total

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