Portal:RenalGenomics
From WikiPathways
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Revision as of 17:51, 14 June 2017
Renal genomics pathways at WikiPathways
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This portal highlights WikiPathways content related to renal biology and disease. Most available pathways lack tissue/cell specificity and are of limited usefulness in highly differentiated organs such as the kidney. In order to produce quality renal genomics data, new and updated kidney-specific pathways are needed. The Renal Genomics Portal offers an opportunity for renal physiologists to participate in creating, testing and curating new pathways, thereby contributing with modern methodology to integrate the renal knowledge-base. |
General Information
About Wikipathways
- WikiPathways Overview
- Bioinformatics tools using WikiPathways Software and Resources
About this portal
- On the right, you'll find a curated set of Featured Pathways, representing renal biology-related pathways at WikiPathways.
- On the left, you'll find a Search box to help find pathways by keywords or gene names.
- Below, you'll find information on how to get involved with pathway curation, to help improve and expand the WikiPathways collection of renal specific pathways.
Renal Pathways Collection
Renal Pathology
- HIPK2 in kidney fibrosis (Homo sapiens)
- Nephrotic syndrome (Homo sapiens)
- Wnt Signaling in Kidney Disease (Homo sapiens) (Mus musculus)
- Polycystic Kidney Disease Pathway (Homo sapiens)
Glom and Podocyte
- Primary Focal Segmental Glomerulosclerosis FSGS (Homo sapiens) (Mus musculus) (Bos taurus)
- PodNet: protein-protein interactions in the podocyte (Mus musculus)
- XPodNet - protein-protein interactions in the podocyte expanded by STRING (Mus musculus)
Proximal Nephron
- Proximal Tubule Transporters (Rattus norvegicus)
- Hexoses Metabolism in Proximal Tubules (Rattus norvegicus)
- Fructose Metabolism in Proximal Tubules (Rattus norvegicus)
- Polyol Pathway (Homo sapiens) (Mus musculus) (Rattus norvegicus) (Bos taurus)
- Lipid Droplet Metabolism (Rattus norvegicus)
Distal Nephron
- Thick Ascending Limb Transport (Rattus norvegicus)
- Angiotensin Signaling in Thick Ascending Limbs (Rattus norvegicus)
- Vasopressin Regulates Renal Water Homeostasis Via Aquaporins (Homo sapiens)
- Distal Convoluted Tubule 1 (DCT1) Cell (Mus musculus)
Renal cell carcinoma
- Pathways in clear cell renal cell carcinoma (Homo sapiens)
- Type 2 papillary renal cell carcinoma (Homo sapiens)
- MET in type 1 papillary renal cell carcinoma (Homo sapiens)
- Hereditary leiomyomatosis and renal cell carcinoma pathway (Homo sapiens)
- Tumor suppressor activity of SMARCB1(Homo sapiens)
Other pathways
- Renin-Angiotensin System (Rattus norvegicus)
- ACE Inhibitor Pathway (Homo sapiens) (Bos taurus)
- Endothelin Pathways (Homo sapiens) (Bos taurus)
- Vitamin D Metabolism (Homo sapiens) (Bos taurus)
- Vitamin D Metabolism II (Homo sapiens)
Pathways under construction
- Tg26 glom (Mus musculus)
Suggested Contributions
- Membranoproliferative Glomerulonephritis type II
- Acute Kidney Injury
- Chronic Kidney Disease
- Diabetic Nephropathy
- Kidney Transplants and Rejection
- Mitochondria in Renal Disease
- Membranous Nephropathy
- Immune System and the Kidney
- Renovascular Hypertension
- Salt-Sensitive Hypertension
Featured Pathway
Nephrotic syndrome (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/a/a3/WP4758_92502.svg:
Status:1
Message:Exception in thread "main" java.lang.NullPointerException
at org.pathvisio.core.Engine.getPathwayImporters(Unknown Source)
at org.pathvisio.core.Engine.importPathway(Unknown Source)
at org.pathvisio.core.util.Converter.main(Unknown Source)
Command:java -Xmx1024M -jar /var/www/wikipathways/wpi/bin/pathvisio_core.jar "/var/www/wikipathways" "/var/www/wikipathways/images/a/a3/WP4758_92502.svg" 2>&1
' in /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php:1255
Stack trace:
- 0 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1227): Pathway::convertWithPathVisio(false, '/var/www/wikipa...')
- 1 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1137): Pathway->saveConvertedByPathVisioCache('svg')
- 2 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1153): Pathway->updateCache('svg')
- 3 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(129): Pathway->getImage()
- 4 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(53): makeThumbLinkObj(Object(Pathway), 'Nephrotic syndr...', 'https://classic...', 'Nephrotic syndr...', 'center', 'pwthumb', '300')
- 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP4758', '300', 'center', 'Nephrotic syndr...', 'pathway', 'Nephrotic syndr...')
- 6 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('renderPathwayIm...', Array)
- 7 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
- 8 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
- 9 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
- 10 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
- 11 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{Template:Toda...')
- 12 /var/www/wikipathways/includes/parser/Parser.php(439): Parser->internalParse('{{Template:Toda...')
- 13 /var/www/wikipathways/wpi/extensions/PathwayOfTheDay/PathwayOfTheDay.php(60): Parser->recursiveTagParse('{{Template:Toda...')
- 14 [internal function]: getPathwayOfTheDay(Object(Parser), 'Friday 3 May 20...', 'Portal:RenalGen...')
- 15 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('getPathwayOfThe...', Array)
- 16 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
- 17 /var/www/wikipathways/includes/parser/Parser.php(2981): PPFrame_DOM->expand(Object(PPNode_DOM))
- 18 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
- 19 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1239): PPFrame_DOM->expand(Object(DOMElement), 4)
- 20 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1247): PPTemplateFrame_DOM->getNamedArgument('contents')
- 21 /var/www/wikipathways/includes/parser/Parser.php(3201): PPTemplateFrame_DOM->getArgument('contents')
- 22 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(934): Parser->argSubstitution(Array, Object(PPTemplateFrame_DOM))
- 23 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
- 24 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
- 25 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
- 26 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
- 27 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
- 28 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{{{FULLPAGENAM...')
- 29 /var/www/wikipathways/includes/parser/Parser.php(321): Parser->internalParse('{{{{FULLPAGENAM...')
- 30 /var/www/wikipathways/includes/OutputPage.php(405): Parser->parse('{{{{FULLPAGENAM...', Object(Title), Object(ParserOptions), true, true, 92537)
- 31 /var/www/wikipathways/includes/OutputPage.php(391): OutputPage->addWikiTextTitle('{{{{FULLPAGENAM...', Object(Title), true, true)
- 32 /var/www/wikipathways/includes/OutputPage.php(500): OutputPage->addWikiTextTitleTidy('{{{{FULLPAGENAM...', Object(Title), true)
- 33 /var/www/wikipathways/includes/DifferenceEngine.php(313): OutputPage->addWikiTextTidy('{{{{FULLPAGENAM...')
- 34 /var/www/wikipathways/includes/DifferenceEngine.php(271): DifferenceEngine->renderNewRevision()
- 35 /var/www/wikipathways/includes/Article.php(729): DifferenceEngine->showDiffPage(false)
- 36 /var/www/wikipathways/includes/Wiki.php(437): Article->view()
- 37 /var/www/wikipathways/includes/Wiki.php(59): MediaWiki->performAction(Object(OutputPage), Object(Article), Object(Title), Object(User), Object(WebRequest))
- 38 /var/www/wikipathways/index.php(93): MediaWiki->initialize(Object(Title), Object(Article), Object(OutputPage), Object(User), Object(WebRequest))
- 39 {main}
View all Featured Pathways for this Portal
Get Involved!!
- Kidney Precision Medicine Project (KPMP): The KPMP actively engages academics, industry, and the broader scientific community as it works to deepen understanding of the kidneys.
- Epithelial System Biology Laboratory(ESBL): this webpage contains links to many relevant renal systems biology studies.
- Kidney System Biology Project (ESBL): this webpage contains links to renal epithelial transcriptome and proteome databases.
- Supported Software: a list with links and description of bioinformatics tools using WikiPathways.
- Other Pathway repositories: KEGG pathways, BioCarta Reactome.
