WikiPathways

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A WIKI FOR BIOLOGICAL PATHWAYS

In the “tradition” of Wikipedia and other wiki platforms, WikiPathways is intended to be an open, public space for content editing dedicated to biological pathways, facilitating the contribution and maintenance of pathway information from the scientific community.

UNDER CONSTRUCTION

This site is not officially open for business. We are still implementing critical features and making major changes to these pages. If you are interested in what this site is about, please feel free to contact us. We plan to have the site up and running by the end of April!

Thomas Kelder: Thomas.Kelder[AT]BIGCAT.unimaas.nl
Alex Pico: apico[AT]gladstone.ucsf.edu

HOW TO FIND A PATHWAY

There are many ways to find your pathways of interest. You can search by:
  • Name of the pathway
  • Browse by species
  • Browse by pathway categories
Coming soon:
  • Search by gene name
  • Advanced search options, limit by organism or category

VIEWING PATHWAYS

Image
Once you are on a Pathway Page you can click on the image of the pathway to view the SVG representation. The pathway image is available for download in SVG and PNG formats.
Text
Each Pathway Page has a text description, itemized gene list, references and relevant links.
Data
Each pathway is also available for download as a GPML data file (GenMAPP Pathway Markup Language), an XML for annotated, curated pathway content. This format can be used with PathVisio. Pathways are also available as .mapp files for use in GenMAPP.

EDITING PATHWAYS

In addition to editing the text fields on a given Pathway Page, this wiki also support the ability to edit the pathway itself! Click on "EDIT" and a webstart version of PathVisio will open with the current pathway loaded. You can then add, edit or delete content from the pathway. When you save, updated version of the images, controlled text, and data files are generated and are immediately available.

Today's featured pathway


Unable to get pathway of the day: FeaturedPathways doesn't contain any valid pathway!


Contents


Overview of all human pathways

Overview of all mouse pathways

Overview of all rat pathways

Cellular Process category

Metabolic Process category

Physiological Process category

Molecular Function category


WikiPathways Statistics


  • There are 2792 pathways
  • Number of pathways (and unique genes) per species:
Anopheles gambiae: 20 (428)
Arabidopsis thaliana: 94 (956)
Bacillus subtilis: 3 (14)
Beta vulgaris: 1 (25)
Bos taurus: 274 (3743)
Caenorhabditis elegans: 66 (882)
Canis familiaris: 112 (2820)
Danio rerio: 105 (2708)
Drosophila melanogaster: 35 (565)
Escherichia coli: 12 (28)
Equus caballus: 12 (200)
Gallus gallus: 100 (2106)
Glycine max: 1 (2)
Gibberella zeae: 2 (0)
Homo sapiens: 1134 (8175)
Hordeum vulgare: 1 (9)
Mus musculus: 226 (4977)
Mycobacterium tuberculosis: 17 (148)
Oryza sativa: 69 (493)
Pan troglodytes: 116 (2937)
Populus trichocarpa: 5 (0)
Rattus norvegicus: 173 (3623)
Saccharomyces cerevisiae: 136 (856)
Solanum lycopersicum: 7 (5)
Sus scrofa: 9 (65)
Vitis vinifera: 1 (0)
Zea mays: 58 (31)
Plasmodium falciparum: 1 (0)
Brassica napus: 2 (162)
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