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9 results for “Cytoscape”
Cytoscape Session file for clusterMaker2
<p>Cytoscape Session file containing STRING protein-protein interaction data with yeast heat shock data from the GEO series GSE18 platform GPL51 (Gasch, et. al., 2000). All results from the BMC Bioinformatics publication were derived from this session file.</p>
Cytoscape files - Systems-level analyses of protein-protein interaction network dysfunctions via epichaperomics identify cancer-specific mechanisms of stress adaptation
<p>Cytoscape files of pathway enrichment analyses and PPI mapping associated with manuscript https://www.nature.com/articles/s41467-023-39241-7</p> <p><strong>Systems-level analyses of protein-protein interaction network dysfunctions via epichaperomics</strong> <strong>identify cancer-specific mechanisms of stress adaptation </strong></p> <p>Anna Rodina<sup>1,11</sup>, Chao Xu<sup>1,11</sup>, Chander S. Digwal<sup>1,11</sup>, Suhasini Joshi<sup>1,11</sup>, Anand R. Santhaseela<sup>1</sup>, Sadik Bay<sup>1</sup>, Swathi Merugu<sup>1</sup>, Aftab Alam<sup>1</sup>, Pengrong Yan<sup>1</sup>, Chenghua Yang<sup>1,12</sup>, Tanaya Roychowdhury<sup>1</sup>, Palak Panchal<sup>1</sup>, Liza Shrestha<sup>1</sup>, Yanlong Kang<sup>1</sup>, Sahil Sharma<sup>1</sup>, Yogita Patel<sup>2</sup>, Justina Almadovar<sup>1</sup>, Adriana Corben<sup>3,13</sup>, Mary Alpaugh<sup>1,14</sup>, Shanu Modi<sup>4</sup>, Monica L. Guzman<sup>5</sup>, Teng Fei<sup>6</sup>, Tony Taldone<sup>1</sup>, Stephen D. Ginsberg<sup>7,8</sup>, Hediye Erdjument-Bromage<sup>9</sup>, Thomas A. Neubert<sup>9</sup>, Katia Manova-Todorova<sup>10</sup>, Jason C. Young<sup>2</sup>,<strong> </strong>Meng-Fu Bryan Tsou<sup>10</sup><strong>, </strong>Tai Wang<sup>1,*</sup>, Gabriela Chiosis<sup>1,4,*</sup></p> <p><strong>Abstract </strong></p> <p>Systems-level assessments of protein-protein interaction (PPI) network dysfunctions are currently out-of-reach because approaches enabling proteome-wide identification, analysis, and modulation of context-specific PPI changes in native (unengineered) cells and tissues are lacking. Herein, we take advantage of first-in-class chemical binders of maladaptive scaffolding structures termed epichaperomes and develop an epichaperome-based ‘omics platform, epichaperomics, to identify PPI alterations in disease. We provide multiple lines of evidence, at both biochemical and functional levels, demonstrating the importance of these probes to identify and study PPI network dysfunctions and provide mechanistically and therapeutically relevant proteome-wide insights. As proof-of-principle, we derive systems-level insight into PPI dysfunctions of cancer cells which enabled the discovery of a context-dependent mechanism by which cancer cells enhance the fitness of mitotic protein networks. Importantly, our systems levels analyses support the use of epichaperome chemical binders as therapeutic strategies aimed at normalizing PPI networks. </p>
Evaluation of Ion Mobility Spectrometry for Improving Constitutional Assignment in Natural Products Mixtures - cytoscape files
<p>Cytoscape files associated with Figure 5 from the manuscript: Evaluation of Ion Mobility Spectrometry for Improving Constitutional Assignment in Natural Products Mixtures</p>
Cytoscape session for the potato knowledge graph extracted with IBM Watson's supervised NLP model
<p>2 cytoscape session files (.cys) representing the genotypic-phenotypic knowledge networks retrieved from scientific literature using IBM Watson. Input to these files were the following: </p> <ul> <li>cytoscapeSession_trainingSet: A training set of 34 full-test articles about potato flesh color</li> <li>cytoscapesession_testSet: A testing set of a 4023 abstracts from PubMed.</li> </ul> <p> </p>
Ergebnisse der Evaluation - Implementing Layout Algorithms Using Cytoscape in ExplorViz
<p>Diese Datei enthält die Ergebnisse der 20 Teilnehmer der Evaluation, die für die Bachelorarbeit durchgeführt wurde</p>
Interactome Analysis: miRNA-gene networks from Austrolebias charrua exposed to Roundup (Cytoscape files .cys)
Open the record for dataset details and reuse information.
The Cytoscape session file for the network of siderophore BGCs predicted from Streptomyces genomes
<p>The Cytoscape session file for the network of siderophore BGCs predicted from Streptomyces genomes</p>
The Cytoscape session file for the network of indole BGCs predicted from Streptomyces genomes
<p>The Cytoscape session file for the network of indole BGCs predicted from Streptomyces genomes</p>
Figure 1 from: Chen R, Yu W (2016) Matrix Proteins and Proteinases Network in Human Cardiovascular Diseases Explored By Cytoscape. Research Ideas and Outcomes 2: e9617. https://doi.org/10.3897/rio.2.e9617
Figure 1 - Cytoscape network, derived from MMP7, ADAM17, SDC, COL1, and VCAN (see Abstract for full spellings of abbreviations).
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.