@NDExProject

Developed @UCSanDiego, NDEx is an open source software infrastructure to store, share and publish biological network knowledge

 La Jolla, CA
ndexbio.org
Joined September 2015
  • Tweets600
  • Following141
  • Followers462
Curious about the current status of @NDExProject ? Wondering how to use our infrastructure or collaborate with us? Find out in our latest video presentation crafted for #ismbeccb2023 ! youtu.be/uyb1kITH0Ns @cytoscape @ucsdccbb @CancerCellMap #NCIITCR
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... However, it is perfectly aware of the recent events involving Credit Suisse...
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According to #ChatGPT , the Silicon Valley Bank collapse never happened, all news about it are fabricated and the sources reporting it (#NBC #abcnews #NPR, #CBS, etc) not legit...
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The NDEx IQuery paper is published in Bioinformatics! Thanks to @xanderpico, @benjamingyori and the whole @NDExProject team for their hard work! Read it now: bit.ly/3L63S0M @WikiPathways @IndraSysBio @sigpathproject @signor_database @cbioportal @cytoscape #nciitcr
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IQuery v1.4 - gene set analysis in numbers: - 972 curated pathways including @WikiPathways (675), @signor_database (90) and @NCIsysbio's PID v2.0 (207) - 6295 @IndraSysBio-assembled GO term networks - 32263 gene sets from @wikipathway's Published Figures OCR project #nciitcr
With its latest v1.4 release, the NDEx Integrated Query (IQuery) offers a novel approach to network/pathway-based gene set interpretation that complements or extends existing resources. It combines novel sources of pathways, integration with Cytoscape, and the ability to store and share analysis results. The IQuery web application performs multiple gene set analyses based on diverse pathways and networks stored in NDEx. These include curated pathways from WikiPathways and SIGNOR, published pathway figures from the last 27 years, machine-assembled networks using the INDRA system, and the new NCI-PID v2.0, an updated version of the popular NCI Pathway Interaction Database. IQuery’s integration with MSigDB and cBioPortal now also provides pathway analysis in the context of these two popular resources.

ALT With its latest v1.4 release, the NDEx Integrated Query (IQuery) offers a novel approach to network/pathway-based gene set interpretation that complements or extends existing resources. It combines novel sources of pathways, integration with Cytoscape, and the ability to store and share analysis results. The IQuery web application performs multiple gene set analyses based on diverse pathways and networks stored in NDEx. These include curated pathways from WikiPathways and SIGNOR, published pathway figures from the last 27 years, machine-assembled networks using the INDRA system, and the new NCI-PID v2.0, an updated version of the popular NCI Pathway Interaction Database. IQuery’s integration with MSigDB and cBioPortal now also provides pathway analysis in the context of these two popular resources.

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Now published!!! Transcriptional regulatory networks of circulating immune cells computed from public clinical #T1D transcriptomic datasets. bit.ly/3P7Cnm7 @NIDDKgov @dkNET_Info @T1DExchange @JDRF @sigpathproject @DiabetesRsrch @cytoscape #diabetes
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Replying to @cbioportal
@cbioportal queries now include #PathwayEnrichment analysis powered by @NDExProject iQuery! Analyze your genes of interest annotated with alteration frequencies in the context of curated pathways from @WikiPathways , @signor_database and NCI-Nature PID. #NCIITCR #networkbiology
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A map showing collaboration among San Diego-based research institutes! Only includes publications in Nature, Science and Cell from 2012 to 2022: bit.ly/35rAHCI Full map: bit.ly/3iQL3z1 @scrippsresearch @sbpdiscovery @ljiresearch @salkinstitute @UCSanDiego
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Replying to @WikiPathways @cytoscape
Please contact us if you are interested in adding the NDEx iQuery search tool to your website or if you know of network and pathway resources you would like to see included in iQuery. And of course, your feedback is always appreciated! ndexbio.org/iquery/
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Curious to learn more about NDEx IQuery and the new gene set analysis added in its v1.3 release? Watch the video poster we presented at the #nciitcr21 annual meeting: youtu.be/mhaPT1ku2Ck @cytoscape #networkbiology @CancerCellMap @IndraSysBio @WikiPathways @signor_database
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Would you like to find figures and publications related to your genes of interest? Just run an NDEx IQuery, then look at the results in the "Pathway Figures" tab... Courtesy of the @WikiPathways team! #nciitcr @cytoscape @CancerCellMap #networkbiology @ucsdccbb @signor_database
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We did it! The NDEx public server and web application are back online, fully functional and updated with the latest release. Please review the NDEx v2.5.1 Release Notes here: bit.ly/34vsMjC #nciitcr @cytoscape @CancerCellMap @ucsdccbb @ucsd_sbrg @WikiPathways
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OUTAGE NOTICE! The NDEx public server and web application will be offline for planned maintenance and update starting on Friday May 28th at 6:00 PM (PDT). The outage will last approximately 4 hours. We apologize for the inconvenience. #nciitcr @CancerCellMap @cytoscape
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