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57 results for “co-expression analysis”
Decoding host-microbiome interactions through co-expression network analysis within the non-human primate intestine
<p>Supplementary Table Captions:</p> <p>Supplementary Table S9. Evaluation and parameter determination of host and microbiome RNA read classification using simulation datasets</p> <p>Supplementary Table S10. 40 pathways significantly upregulated in the cecum as compared to the transverse colon</p> <p>Supplementary Table S11. Host-microbiome gene co-expression network edges</p> <p>Supplementary Table S12. Host-host gene co-expression network edges</p> <p>Supplementary Table S13. Microbiome-microbiome gene co-expression network edges</p> <p>Supplementary Table S14. List of genes included in each gene module identified from the gene co-expression network</p> <p>Supplementary Table S15. Results of enrichment analysis for each gene module identified from the gene co-expression network</p> <p>Supplementary Table S16. The top 32 bacterial species in terms of expression abundance based on metatranscriptome profiles</p> <p>Supplementary Table S17. Number of microbiome RNA reads annotated by the KEGG database</p> <p>Supplementary Table S18. Results of enrichment analysis of gene modules for each parameter</p> <p>Supplementary Table S19. Evaluation of modules in each parameter of Newman algorithm</p> <p>Supplementary Table S20. Evaluation of modules in each parameter of Louvain algorithm</p> <p>Supplementary Table S21. Evaluation of modules in each parameter of Leiden algorithm</p> <p>Supplementary Table S22. Evaluation of modules in each parameter of WGCNA</p>
Dataset for a Mouse and Rat heart trancriptomic and co-expression network analysis
<ul> <li>mouse_heart_data and rat_heart_expression contain GEO expression matrix for mouse and rat experiments.</li> <li>gse_gsm_mouse.txt and gse_gsm_rat.txt contain experiment IDs and series IDs from GEO.</li> <li>heart_quantNormData_mouse.tsv and heart_quantNormData_rat.tsv contain normalised expression matrices.</li> <li>heart_quantNormData_mouse_1sd.tsv and heart_quantNormData_rat_1sd.tsv contain the normalised expression matrices restricted to genes with a standard deviation higher than 1.</li> <li>fileForSCHypeThreshold0.5_heart.txt and fileForSCHypeThreshold0.75_heart.txt are the input for SCHype. schype_output_0.5th_heart.nodes.txt, schype_output_0.5th_heart.edges.txt, schype_output_0.75th_heart.nodes.txt and schype_output_0.75th_heart.edges.txt are the outputs.</li> <li>geneLists.zip contains gene lists used for ontology analysis (ENSEMBL gene id)</li> </ul>
Supplemental Information on the Weighted Gene Co-expression Network Analysis performed for the work "Time-resolved oxidative signal convergence across the algae–embryophyte divide"
<p>Supplemental Information on the Weighted Gene Co-expression Network Analysis (WGNCA) performed for the work "Time-resolved oxidative signal convergence across the algae–embryophyte divide"</p> <p>The results are sorted by the three species analysed: the two algae <em><span>Zygnema circumcarinatum</span></em><span> SAG 698-1b (<em>Zygnema</em>) and <em>Mesotaenium endlicherianum </em></span><span>SAG 12.97 (<em>Mesotaenium</em>); and the bryophyte <em>Physcomitrium patens</em></span><span><em> </em>strain Gransden 2004 (<em>Physcomitrium</em>).</span></p>
Network analysis reveals rare disease signatures across multiple levels of biological organization - Co-expression dataset
<p>The GTEx-derived co-expression data in 38 tissues generated in Buphamalai et.al., Network analysis reveals rare disease signatures across multiple levels of biological organization, Nature Communications 2021. Please see the publication's Methods section for details.</p>
Meta-analysis of scRNA-seq Co-expression in Human Neural Organoids Reveals High Variability in Recapitulating Primary Tissue
<p>Contains all code and data for Werner and Gillis, Meta-analysis of scRNA-seq Co-expression in Human Neural Organoids Reveals High Variability in Recapitulating Primary Tissue, 2024. </p> <p>Additionally, the code and data for this paper can be found at https://github.com/JonathanMWerner/meta_organoid_analysis with an easy to view github markdown file containing all the code used to generate all figure panel plots at https://github.com/JonathanMWerner/meta_organoid_analysis/blob/main/figure_plots_with_data_code.md.</p> <p>Due to file size limits on github, there are several data files not available on github, but are available here on zenodo in the data_for_plots.zip file, see below:</p> <pre>umap_embeddings_Fig2A.Rdata<br>cross_dataset_aggregated_exp_metaMarker_all_fetal_SuppFig1B_Fig2E.Rdata<br>organoid_egad_results_ranked_6_26_24_Fig3D.Rdata<br>fetal_egad_results_ranked_6_26_24_Fig3D.Rdata<br>org_eigenvec_matrices_SuppFig3CD.Rdata</pre> <p><br>The R package developed for this paper is available at https://github.com/JonathanMWerner/preservedCoexp</p>
Data from: Determinants and co-expression of anti-predator responses in amphibian tadpoles: a meta-analysis
A wide range of taxa respond to perceived predation risk (PPR) through inducible defenses, and many prey are capable of responding both behaviorally and morphologically to the same risk event. In cases where multiple defenses confer protection by independent means (i.e., they are mechanistically independent) responses will either be co-expressed, or the expression of one defense will limit the capacity (or need) to respond along another axis. Our ability to generate a broad understanding of these patters has been limited, in part, by difficulties in comparing results across studies that employ distinct experimental protocols. Using the extensive literature on tadpole responses to PPR, we conducted a meta-analysis to identify the ecological and experimental determinants of inducible defence expression. We then assessed whether the magnitude of response to PPR along behavioural versus morphological response axes was positively, or negatively, correlated. The most commonly quantified responses to perceived risk in tadpoles included reductions in movement and swimming behaviour, and altered tail morphology. Our analyses reveal that tadpole behavioural responses are strongly influenced by prey family, predator taxon, evolutionary history with the predator (native vs. non-native), amount of prey consumed by the predator, and how perceived risk was manipulated (e.g., presence vs. absence of alarm cues). Tail morphology was similarly influenced by these factors, but also whether the target prey was palatable to predators. Thus, our results identify ecological and experimental features that critically influence the observed effect size in tadpole responses to PPR. A positive correlation between behavioural and morphological responses in studies where both were measured indicates that trait co-specialization is the predominant pattern of defense deployment in larval amphibians. This positive relationship suggests that survival tends to be maximized in tadpoles through equivalent coactivation of multiple independent axes of protection, opposed to maximal expression along any single axis.
Data from: Analysis of gene expression in rheumatoid arthritis and related conditions offers insights into sex-bias, gene biotypes and co-expression patterns
Open the record for dataset details and reuse information.
Data from: Determinants and co-expression of anti-predator responses in amphibian tadpoles: a meta-analysis
Open the record for dataset details and reuse information.
Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution
GEO Series GSE46915. Caulobacter vibrioides. 15 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide analysis of RNA binding proteins co-expression with alternative splicing events in mitral valve prolapse
GEO Series GSE229778. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing.
A co-expression analysis of the placental transcriptome in association with maternal pre-pregnancy BMI and newborn birth weight
GEO Series GSE128381. Homo sapiens. 183 samples. Type: Expression profiling by array.
Transcriptome profiling and co-expression network analysis of 96 Haematococcus pluvialis samples
GEO Series GSE289633. Haematococcus lacustris. 96 samples. Type: Expression profiling by high throughput sequencing.
Comprehensive analysis of the mRNA-lncRNA co-expression profile and ceRNA networks patterns in chronic hepatitis B
GEO Series GSE136343. Homo sapiens. 9 samples. Type: Expression profiling by array.
Co-expression analysis reveals distinct alliances around two carbon fixation pathways in hydrothermal vent symbionts
GEO Series GSE249345. Candidatus Endoriftia persephonae. 30 samples. Type: Expression profiling by high throughput sequencing.
Weighted gene co-expression network analysis on microarray data from subregions of zebra finch (Taeniopygia guttata) basal ganglia
GEO Series GSE34819. Taeniopygia guttata. 54 samples. Type: Expression profiling by array.
Systematic identification and analysis of light-responsive circular RNA and co-expression networks in lettuce (Lactuca sativa)
GEO Series GSE148578. Lactuca sativa. 9 samples. Type: Expression profiling by high throughput sequencing.
Analysis of gene co-expression networks in skin cells exposed to different doses of ionising radiation at different time points
GEO Series GSE29344. Homo sapiens. 24 samples. Type: Expression profiling by array.
Transcriptome analysis and weighted gene co-expression network reveal candidate genes and pathways responses to lactate dehydrogenase inhibition (oxamate) in hyperglycemic human renal proximal epithel
GEO Series GSE182138. Homo sapiens. 5 samples. Type: Expression profiling by high throughput sequencing.
Co-expression network analysis from genes involved with neural-differentiation shows specific pattern in patients with schizophrenia
GEO Series GSE62105. Homo sapiens. 11 samples. Type: Expression profiling by array.
Co-expression analysis reveals gene cluster associated with methylation of enhancers and chromosomal instability under TP63 and TRIM29 regulation [RNA-seq]
GEO Series GSE204811. Homo sapiens. 13 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.