• 380632084612552190316041959032913770543347PublicAssets/3732
    A molecular interaction network in yeast 2
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    A molecular interaction network in yeast 2

    3732

    The image visualizes a part of the yeast molecular interaction network. The lines in the network represent connections among genes (shown as little dots) and different-colored networks indicate subnetworks, for instance, those in specific locations or pathways in the cell. Researchers use gene or protein expression data to build these networks; the network shown here was visualized with a program called Cytoscape. By following changes in the architectures of these networks in response to altered environmental conditions, scientists can home in on those genes that become central "hubs" (highly connected genes), for example, when a cell encounters stress. They can then further investigate the precise role of these genes to uncover how a cell's molecular machinery deals with stress or other factors. Related to images 3730 and 3733.
    Public Note
    Internal NoteFrom: Keiichiro Ono [mailto:keiono@gmail.com] Sent: Wednesday, January 27, 2016 1:02 PM To: Machalek, Alisa Zapp (NIH/NIGMS) [E] Cc: Trey Ideker Subject: Re: seeking Cytoscape images Sorry for slow replay. Yes, I usually distribute all documents and images under CC-by license: https://creativecommons.org/licenses/by/4.0/ I think this is almost same as PD. All of the network visualizations are generated from same yeast network distributed with Cytoscape. It is an (old) subnetwork from BIND interaction database. http://cl.ly/bfUV -- structure-aware-layout - Sample visualization of substructure of the yeast network. Communities (modules) are calculated with this algorithm: http://igraph.org/r/doc/cluster_fast_greedy.html And visualized with Cytoscape and cyREST (https://github.com/cytoscape/cyREST). The entire workflow is available as this R script: https://github.com/idekerlab/cy-rest-R/blob/develop/workflow1_structure_based_visualization.R http://cl.ly/bd38 --com4 - Same result visualized with other Style in Cytoscape. http://cl.ly/bbQb --community1 Subnetwork of the original one. Please let me know if you have any questions. Thanks, Kei
    Keywords
    SourceKeiichiro Ono, UCSD
    Date2016-01-28 00:00:00
    Credit LineKeiichiro Ono and Trey Ideker, UCSD
    InvestigatorTrey Ideker, UCSD
    Record TypeIllustration
    Topic Area(s);#Genes;#Tools and Techniques;#
    Previous Uses
    StatusActive

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