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Dataset results
193 results for “co-expression”
Three TF Gene Co-expression Modules are involved in Pressure-Overload Cardiac Hypertrophy in Male Mice (microRNA)
GEO Series GSE99459. Mus musculus. 20 samples. Type: Non-coding RNA profiling by array.
Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization
GEO Series GSE32677. Homo sapiens. 3 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
A systems approach implicates a brain mitochondrial oxidative homeostasis co-expression network in genetic vulnerability to alcohol withdrawal
GEO Series GSE89281. Mus musculus. 32 samples. Type: Expression profiling by array.
Co-expression clustering across flower development identifies modules for diverse floral forms in Achimenes (Gesneriaceae)
<p>Data and code for the analyses published in:</p> <p>Roberts WR, Roalson EH. 2020. Co-expression clustering across flower development identifies modules for diverse floral forms in <em>Achimenes</em> (Gesneriaceae). <em>PeerJ</em>. In Press.</p>
Co-expression trans-eQTL analysis data
<p><strong>Sample metadata:</strong></p> <ul> <li>sample_metadata.tsv - tab separated file with metadata for samples used in this analysis.</li> </ul> <p><strong>Gene expression matrix:</strong></p> <ul> <li>Merged_ENSG_expression.tsv - integrated gene expression matrix used in the co-expression analysis (Ensembl IDs in rows and sample IDs in columns). The matrix can be split into sub matrices using the metadata from sample_metadata.tsv for separate analysis of cell types.</li> </ul> <p><strong>Genes in the modules:</strong></p> <ul> <li>ICA_modules.tsv - data for assigning genes to modules from ICA method. Column 'loading' shows the contribution value of the gene to the module. Column 'approach' indicates if the module was detected from integrated or separate data. Column 'qtl_group' is an identifier for the cell type/condition.</li> <li>PEER_modules.tsv - data for assigning genes to modules from PEER method. Column 'loading' shows the contribution value of the gene to the module. </li> <li>PLIER_modules.tsv - data for assigning genes to modules from PLIER method. Column 'loading' shows the contribution value of the gene to the module.</li> <li>WGCNA_modules.tsv - data for assigning genes to modules from WGCNA method. Column 'loading' shows the contribution value of the gene to the module. Column 'loading' has value 1 as the method assigns genes to modules without defining their contributions. </li> <li>funcExplorer_modules.tsv - data for assigning genes to modules from funcExplorer method. Column 'loading' has value 1 as the method assigns genes to modules without defining their contributions. </li> </ul> <p><strong>Module eigenvectors used for the trans-eQTL analysis</strong></p> <ul> <li>eigenvectors_integrated.tsv - module eigenvectors for all the co-expression analysis methods applied to integrated data</li> <li>eigenvectors_separate.tsv- module eigenvectors for all the co-expression analysis methods applied to cell types separately</li> </ul> <p><strong>SuSiE fine mapping credible sets </strong></p> <ul> <li>SuSiE_credible_sets_integrated.tsv</li> <li>SuSiE_credible_sets_separate.tsv</li> </ul>
Gene expression and co-expression matrix for diatoms
<p>Supplemental dataset accompanying the paper: Comprehensive and functional analysis of horizontal gene transfer events in diatoms, Vancaester et al. MBE (<a href="https://doi.org/10.1093/molbev/msaa182">https://doi.org/10.1093/molbev/msaa182</a>).</p> <p>This dataset contains the generated gene expression matrix for the diatoms <em>Phaeodactylum tricornutum</em>, <em>Seminavis robusta</em>, <em>Fragilariopsis cylindrus</em> and <em>Thalassiosira pseudonana</em>. Relevant experiments were queried using Curse (Vaneechoutte and Vandepoele 2019), which also allows the user to identify and curate replicates. Next, the atlas was generated using Prose (Vaneechoutte and Vandepoele 2019), which uses the SRA toolkit to download the raw data locally, FastQC (Andrews 2010) to perform quality control and adapter detection, Trimmomatic (Bolger et al. 2014) for automatic read trimming and finally kallisto (Bray et al. 2016) for expression quantification in transcripts per million (TPM). Finally, also the co-expression clusters defined based on the gene expression for <em>Phaeodactylum tricornutum </em>is included.</p> <p>The dataset containing all detected phylogenetic trees of diatom genes of horizontal descent can be found on <a href="https://zenodo.org/record/3889669#.XyB-E-dCdPY">(https://zenodo.org/record/3889669#.XyB-E-dCdPY)</a>.</p>
Identification of Potential Functional Modules and Diagnostic Genes for Crohn's Disease Based on Weighted Gene Co-expression Network Analysis and LASSO Algorithm
<p>Table S1 651 DEGs between CD and control samples</p> <p>Table S2 381 ME turquoise module genes</p> <p>Table S3 Coefficients of the eight module genes analyzed by LASSO regression</p>
The raw data about the research of identification of biomarkers related to systemic sclerosis with or without pulmonary hypertension via co-expression analysis
<p>This file includes some of necessary raw data and code about the research of identification of biomarkers related to systemic sclerosis with or without pulmonary hypertension via co-expression analysis.</p> <p> </p>
Dataset for "Decoding host-microbiome interactions through co-expression network analysis within the non-human primate intestine"
<p>Dataset:</p> <p>Data1. Host gene expression profile</p> <p>Data2. Microbiome gene expression profile</p>
A Clinical Trial Evaluating the Effect of ASLAN001 in Patients With Recurrent/Metastatic Gastric Cancer Whose Tumors Are Either HER-2 Amplified or Co-expressing HER-1 and HER-2
ClinicalTrials.gov study NCT01614522. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Claudin18.2-redirected Chimeric Antigen Receptor T Cells With Co-expression of Cytokines in Solid Tumors
ClinicalTrials.gov study NCT05393986. IPD Sharing: NO. Countries: 1. Publications: 0.
Two-Part, Phase Ib/II, Open Label, Single-Arm, Multi-center Study to Evaluate the Safety and Efficacy of Varlitinib in Combination With Weekly Paclitaxel in EGFR/HER2 Co-expressing Advanced or Metasta
ClinicalTrials.gov study NCT05400915. IPD Sharing: NO. Countries: 1. Publications: 0.
Pan-T Booster Co-expressing MSLN CAR T Cell Therapy in Advanced/Metastatic Solid Tumors
ClinicalTrials.gov study NCT05693844. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Study of Kappa Chimeric Antigen Receptor (CAR) T Lymphocytes Co-Expressing the Kappa and CD28 CARs for Relapsed/Refractory Kappa+ Non-Hodgkin Lymphoma and Chronic Lymphocytic Leukemia/Small Lymphocyti
ClinicalTrials.gov study NCT04223765. IPD Sharing: NO. Countries: 1. Publications: 0.
Neuromodulatory co-expression in cardiac vagal motor neurons of the Dorsal Motor Nucleus of the Vagus [10x scRNA]
GEO Series GSE260849. Rattus norvegicus. 4 samples. Type: Expression profiling by high throughput sequencing.
Transcription Factor Co-Expression Mediates Lineage Priming for Embryonic and Extra-Embryonic Differentiation [CUT&RUN]
GEO Series GSE227886. Mus musculus. 53 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Stress dynamically regulates co-expression networks of glucocorticoid receptor-dependent MDD and SCZ risk genes.
GEO Series GSE149074. Mus musculus. 384 samples. Type: Expression profiling by high throughput sequencing.
Platelet microRNA-mRNA Co-Expression Profiles Correlate with Platelet Reactivity
GEO Series GSE27917. Rattus norvegicus; Murid gammaherpesvirus 4; Betapolyomavirus hominis; Homo sapiens; Human alphaherpesvirus 1; Human betaherpesvirus 5; human gammaherpesvirus 4; Betapolyomavirus macacae; Mus musculus; Murid betaherpesvirus 1; JC polyomavirus; Human immunodeficiency virus 1; Human gammaherpesvirus 8. 19 samples. Type: Non-coding RNA profiling by array.
Exploring Camelina sativa lipid metabolism regulation by combining gene co-expression and DNA affinity purification analyses
GEO Series GSE184283. Camelina sativa. 41 samples. Type: Other; Expression profiling by high throughput sequencing.
CCR1 and CCR2 co-expression on monocytes is nonredundant and delineates a distinct monocyte subpopulation.
GEO Series GSE251648. Mus musculus. 20 samples. Type: Expression profiling by high throughput sequencing.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.