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Dataset results
8 results for “Protein-Protein Networks”
HDAC6 protein-protein interaction network in CNS
<p>HDAC6 stands out as a distinctive member within the histone deacetylase family due to its predominant presence in the cytosol, facilitating its interaction with a wide array of non-histone proteins. Its dysregulation has been linked to various outcomes, encompassing diverse cancer types, immune-related disorders, and neurological conditions, including Alzheimer's, Parkinson's, ALS, Huntington's, Charcot-Marie-Tooth disease, and Rett syndrome.</p><p>The current network represents the known HDAC6 interactions in the central nervous system (CNS).</p><p>The latest version of the current network is available in WikiPathways under accession number WP5426.</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>
A human IgSF cell-surface interactome reveals a complex network of protein-protein interactions
<p>Cell-surface protein-protein interactions (PPIs) mediate cell-cell communication, recognition and responses. We executed an interactome screen of 564 human cell-surface and secreted proteins, most of which are immunoglobulin superfamily (IgSF) proteins, using a high-throughput, automated ELISA-based screening platform employing a pooled-protein strategy to test all 318,096 PPI combinations. Screen results, augmented by phylogenetic homology analysis, revealed ~380 previously unreported PPIs. We validated a subset using surface plasmon resonance and cell binding assays. Observed PPIs reveal a large and complex network of interactions both within and across biological systems. We identified new PPIs for receptors with well-characterized ligands, and binding partners for 'orphan' receptors. New PPIs include proteins expressed on multiple cell types, and involved in diverse processes including immune and nervous system development and function, differentiation/proliferation, metabolism, vascularization, and reproduction. These PPIs provide a resource for further biological investigation into their functional relevance, and may offer new therapeutic drug targets.</p>
STRING protein-protein interaction network (v11.5)
<p>STRING protein-protein interaction network was downloaded from the STRING website (https://string-db.org/cgi/download?sessionId=bIAz6gR8tk72).</p> <p>Version: 11.5</p>
Predicting the pro-longevity or anti-longevity effect of model organism genes with enhanced Gaussian noise augmentation-based contrastive learning on protein-protein interaction networks
<p>The datasets used to evaluate Enhanced Gaussian noise augmentation-based contrastive learning (EGsCL) against predicting the pro-longevity or anti-longevity effect of model organism gene. This repo also includes the pretrained encoders that obtained the best predictive performance for each organism (see Table 2).</p>
A human IgSF cell-surface interactome reveals a complex network of protein-protein interactions
Open the record for dataset details and reuse information.
Dataset accompanying "SECAT: Quantifying differential protein-protein interaction states by network-centric analysis"
<p>This repository contains input data, processing parameters and results associated with manuscript "SECAT: Quantifying differential protein-protein interaction states by network-centric analysis".</p> <p>Each archive contains a README.txt file that describes the contents.</p> <p>SECAT_scripts_data.tar.xz is an archive containing the scripts and data to generate the manuscript figures.</p>
Patterns of cancer development and progression in the protein-protein interaction network
GEO Series GSE31180. Homo sapiens. 4 samples. Type: Expression profiling by array.
ScienceDex guides
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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.