R36R54 last accessed: 2022-11-04

gemma
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:01.640079

Other names: Tools and database for meta-analysis of functional genomics data, gemma

Gemma is a database for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles. Gemma contains data from thousands of public studies, referencing thousands of published papers. Users can search, access and visualize co-expression and differential expression results.

Webpage:

http://www.chibi.ubc.ca/Gemma

Licence:

Name: Copyrights
URL: https://pavlidislab.github.io/Gemma/terms.html#3-ownership-and-use-restriction

Publications:

Publications
More detailed information about this field from each metasource.

Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data
PMID: 22782548
metasource: Fairsharing.org
version: FAIRsharing.org: Gemma; Gemma; DOI: https://doi.org/10.25504/FAIRsharing.t98nav; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

Application and evaluation of automated semantic annotation of gene expression experiments
PMID: 19376825
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:01.640079

Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data PubMed citations: 56.

56 articles citing: Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data

Un-biased housekeeping gene panel selection for high-validity gene expression analysis. PMID:35853974
SFARI genes and where to find them; modelling Autism Spectrum Disorder specific gene expression dysregulation with RNA-seq data. PMID:35710789
Elucidating gene expression patterns across multiple biological contexts through a large-scale investigation of transcriptomic datasets. PMID:35705903
SigCom LINCS: data and metadata search engine for a million gene expression signatures. PMID:35524556
Differential analysis of binarized single-cell RNA sequencing data captures biological variation. PMID:34988441
TopoFun: a machine learning method to improve the functional similarity of gene co-expression modules. PMID:34761220
Experiment level curation of transcriptional regulatory interactions in neurodevelopment. PMID:34665801
Evaluation of connectivity map shows limited reproducibility in drug repositioning. PMID:34475469
Construction of a Potentially Functional circRNA-miRNA-mRNA Network in Intervertebral Disc Degeneration by Bioinformatics Analysis. PMID:34395625
Genetic influences on hub connectivity of the human connectome. PMID:34244483
Single-cell co-expression analysis reveals that transcriptional modules are shared across cell types in the brain. PMID:34015329
Curation of over 10 000 transcriptomic studies to enable data reuse. PMID:33599246
Co-expression of calcium and hERG potassium channels reduces the incidence of proarrhythmic events. PMID:33002116
Mega-Analysis of Gene Expression in Mouse Models of Alzheimer's Disease. PMID:31767574
RNA-seq data in pain research-an illustrated guide. PMID:31219951
Predictability of human differential gene expression. PMID:30846554
The Cortical Neuroimmune Regulator TANK Affects Emotional Processing and Enhances Alcohol Drinking: A Translational Study. PMID:30721969
Foundry: a message-oriented, horizontally scalable ETL system for scientific data integration and enhancement. PMID:30576493
LCE: an open web portal to explore gene expression and clinical associations in lung cancer. PMID:30532070
Transcriptomic Evidence for Alterations in Astrocytes and Parvalbumin Interneurons in Subjects With Bipolar Disorder and Schizophrenia. PMID:30177255
C-terminal truncation of IFN-γ inhibits proinflammatory macrophage responses and is deficient in autoimmune disease. PMID:29925830
Differential Connectivity in Colorectal Cancer Gene Expression Network. PMID:29843204
Correlated Gene Expression and Anatomical Communication Support Synchronized Brain Activity in the Mouse Functional Connectome. PMID:29789379
BioDataome: a collection of uniformly preprocessed and automatically annotated datasets for data-driven biology. PMID:29688366
The observed alteration in BCL2 expression following lithium treatment is influenced by the choice of normalization method. PMID:29686228
Hub connectivity, neuronal diversity, and gene expression in the Caenorhabditis elegans connectome. PMID:29432412
A publicly available benchmark for biomedical dataset retrieval: the reference standard for the 2016 bioCADDIE dataset retrieval challenge. PMID:29220453
Cross-Laboratory Analysis of Brain Cell Type Transcriptomes with Applications to Interpretation of Bulk Tissue Data. PMID:29204516
Strength of functional signature correlates with effect size in autism. PMID:28687074
PathOS: a decision support system for reporting high throughput sequencing of cancers in clinical diagnostic laboratories. PMID:28438193
Protease-Inhibitor Interaction Predictions: Lessons on the Complexity of Protein-Protein Interactions. PMID:28385878
Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction. PMID:27467773
DNA methylation signature of human fetal alcohol spectrum disorder. PMID:27358653
Exploiting single-cell expression to characterize co-expression replicability. PMID:27165153
Interactive Exploration, Analysis, and Visualization of Complex Phenome-Genome Datasets with ASPIREdb. PMID:27158917
Ontology-based annotations and semantic relations in large-scale (epi)genomics data. PMID:27142216
AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression. PMID:27082953
Meta-Analysis of Gene Expression Patterns in Animal Models of Prenatal Alcohol Exposure Suggests Role for Protein Synthesis Inhibition and Chromatin Remodeling. PMID:26996386
A transcriptional signature of hub connectivity in the mouse connectome. PMID:26772314
Mapping DNA methylation across development, genotype and schizophrenia in the human frontal cortex. PMID:26619358
An interactive web application for the dissemination of human systems immunology data. PMID:26088622
Meta-Analysis of Gene Expression in Autism Spectrum Disorder. PMID:25720351
Network-based metaanalysis identifies HNF4A and PTBP1 as longitudinally dynamic biomarkers for Parkinson's disease. PMID:25646437
A systems-level approach to parental genomic imprinting: the imprinted gene network includes extracellular matrix genes and regulates cell cycle exit and differentiation. PMID:25614607
Differential Co-Expression between α-Synuclein and IFN-γ Signaling Genes across Development and in Parkinson's Disease. PMID:25493648
Meta-analysis of human methylomes reveals stably methylated sequences surrounding CpG islands associated with high gene expression. PMID:25493099
Addiction and reward-related genes show altered expression in the postpartum nucleus accumbens. PMID:25414651
High-throughput DNA analysis shows the importance of methylation in the control of immune inflammatory gene transcription in chronic periodontitis. PMID:25147584
Semantic Web repositories for genomics data using the eXframe platform. PMID:25093072
The inferred cardiogenic gene regulatory network in the mammalian heart. PMID:24971943
De novo mutations in schizophrenia implicate chromatin remodeling and support a genetic overlap with autism and intellectual disability. PMID:24776741
An integrative modeling framework reveals plasticity of TGF-β signaling. PMID:24618419
INMEX--a web-based tool for integrative meta-analysis of expression data. PMID:23766290
Neurocarta: aggregating and sharing disease-gene relations for the neurosciences. PMID:23442263
CancerMA: a web-based tool for automatic meta-analysis of public cancer microarray data. PMID:23241162
InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor. PMID:23158523
Application and evaluation of automated semantic annotation of gene expression experiments PubMed citations: 5.

5 articles citing: Application and evaluation of automated semantic annotation of gene expression experiments

Applying MetaMap to Medline for identifying novel associations in a large clinical dataset: a feasibility analysis. PMID:24928177
InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor. PMID:23158523
Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data. PMID:22782548
Human gene correlation analysis (HGCA): a tool for the identification of transcriptionally co-expressed genes. PMID:22672625
Immune response and mitochondrial metabolism are commonly deregulated in DMD and aging skeletal muscle. PMID:22096509

Tags:

Tags
More detailed information about this field from each metasource.

co-expression
metasource: Fairsharing.org
version: FAIRsharing.org: Gemma; Gemma; DOI: https://doi.org/10.25504/FAIRsharing.t98nav; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

differential gene expression analysis
metasource: Fairsharing.org
version: FAIRsharing.org: Gemma; Gemma; DOI: https://doi.org/10.25504/FAIRsharing.t98nav; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

geeq
metasource: re3data.org
version: re3data.org: Gemma; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R36R54 last accessed: 2022-11-04

fly
metasource: re3data.org
version: re3data.org: Gemma; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R36R54 last accessed: 2022-11-04

functional genomics
metasource: re3data.org
version: re3data.org: Gemma; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R36R54 last accessed: 2022-11-04

gene expression
metasource: re3data.org
version: re3data.org: Gemma; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R36R54 last accessed: 2022-11-04

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:01.640079

gene expression experiment quality
metasource: re3data.org
version: re3data.org: Gemma; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R36R54 last accessed: 2022-11-04

genomics
metasource: re3data.org
version: re3data.org: Gemma; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R36R54 last accessed: 2022-11-04

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:01.640079

human
metasource: re3data.org
version: re3data.org: Gemma; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R36R54 last accessed: 2022-11-04

mouse
metasource: re3data.org
version: re3data.org: Gemma; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R36R54 last accessed: 2022-11-04

rat
metasource: re3data.org
version: re3data.org: Gemma; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R36R54 last accessed: 2022-11-04

worm
metasource: re3data.org
version: re3data.org: Gemma; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R36R54 last accessed: 2022-11-04

zebrafish
metasource: re3data.org
version: re3data.org: Gemma; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R36R54 last accessed: 2022-11-04

genetics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:01.640079

co-expression differential gene expression analysis geeq fly functional genomics gene expression gene expression experiment quality genomics human mouse rat worm zebrafish genetics

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