MicroArray Gene Expression Tabular Format
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MicroArray Gene Expression Tabular Format
metasource: Fairsharing.org
version: FAIRsharing.org: MAGE-TAB; MicroArray Gene Expression Tabular Format; DOI: https://doi.org/10.25504/FAIRsharing.ak8p5g; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
MAGE-TAB
metasource: Fairsharing.org
version: FAIRsharing.org: MAGE-TAB; MicroArray Gene Expression Tabular Format; DOI: https://doi.org/10.25504/FAIRsharing.ak8p5g; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
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MicroArray Gene Expression Tabular Format
metasource: Fairsharing.orgversion: FAIRsharing.org: MAGE-TAB; MicroArray Gene Expression Tabular Format; DOI: https://doi.org/10.25504/FAIRsharing.ak8p5g; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
MAGE-TAB
metasource: Fairsharing.orgversion: FAIRsharing.org: MAGE-TAB; MicroArray Gene Expression Tabular Format; DOI: https://doi.org/10.25504/FAIRsharing.ak8p5g; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
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MicroArray Gene Expression Tabular Format
metasource: Fairsharing.orgversion: FAIRsharing.org: MAGE-TAB; MicroArray Gene Expression Tabular Format; DOI: https://doi.org/10.25504/FAIRsharing.ak8p5g; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
MAGE-TAB
metasource: Fairsharing.orgversion: FAIRsharing.org: MAGE-TAB; MicroArray Gene Expression Tabular Format; DOI: https://doi.org/10.25504/FAIRsharing.ak8p5g; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
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Sharing of microarray data within the research community has been greatly facilitated by the development of the disclosure and communication standards MIAME and MAGE-ML by the FGED Society. However, the complexity of the MAGE-ML format has made its use impractical for laboratories lacking dedicated bioinformatics support. We propose a simple tab-delimited, spreadsheet-based format, MAGE-TAB, which will become a part of the MAGE microarray data standard and can be used for annotating and communicating microarray data in a MIAME compliant fashion. MAGE-TAB will enable laboratories without bioinformatics experience or support to manage, exchange and submit well-annotated microarray data in a standard format using a spreadsheet. The MAGE-TAB format is self-contained, and does not require an understanding of MAGE-ML or XML
Description
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Sharing of microarray data within the research community has been greatly facilitated by the development of the disclosure and communication standards MIAME and MAGE-ML by the FGED Society. However, the complexity of the MAGE-ML format has made its use impractical for laboratories lacking dedicated bioinformatics support. We propose a simple tab-delimited, spreadsheet-based format, MAGE-TAB, which will become a part of the MAGE microarray data standard and can be used for annotating and communicating microarray data in a MIAME compliant fashion. MAGE-TAB will enable laboratories without bioinformatics experience or support to manage, exchange and submit well-annotated microarray data in a standard format using a spreadsheet. The MAGE-TAB format is self-contained, and does not require an understanding of MAGE-ML or XML
metasource: Fairsharing.orgversion: FAIRsharing.org: MAGE-TAB; MicroArray Gene Expression Tabular Format; DOI: https://doi.org/10.25504/FAIRsharing.ak8p5g; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Webpage:
http://fged.org/projects/mage-tab/Webpage
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http://fged.org/projects/mage-tab/
metasource: Fairsharing.orgversion: FAIRsharing.org: MAGE-TAB; MicroArray Gene Expression Tabular Format; DOI: https://doi.org/10.25504/FAIRsharing.ak8p5g; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Publications:
Publications
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A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
PMID: 17087822
metasource: Fairsharing.org
version: FAIRsharing.org: MAGE-TAB; MicroArray Gene Expression Tabular Format; DOI: https://doi.org/10.25504/FAIRsharing.ak8p5g; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Publications
More detailed information about this field from each metasource.
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
PMID: 17087822
metasource: Fairsharing.org
version: FAIRsharing.org: MAGE-TAB; MicroArray Gene Expression Tabular Format; DOI: https://doi.org/10.25504/FAIRsharing.ak8p5g; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
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A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
PubMed citations: 104.
104 articles citing: A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
MITI minimum information guidelines for highly multiplexed tissue images. PMID:35277708
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. PMID:34723319
A proteomics sample metadata representation for multiomics integration and big data analysis. PMID:34615866
ISA API: An open platform for interoperable life science experimental metadata. PMID:34528664
An integrated landscape of protein expression in human cancer. PMID:33893311
A Minimal Information Model for Potential Drug-Drug Interactions. PMID:33762928
From ArrayExpress to BioStudies. PMID:33211879
Toward a Sample Metadata Standard in Public Proteomics Repositories. PMID:32786688
Enabling reusability of plant phenomic datasets with MIAPPE 1.1. PMID:32171029
All of gene expression (AOE): An integrated index for public gene expression databases. PMID:31978081
TACITuS: transcriptomic data collector, integrator, and selector on big data platform. PMID:31757212
ArrayExpress update - from bulk to single-cell expression data. PMID:30357387
DDBJ update: the Genomic Expression Archive (GEA) for functional genomics data. PMID:30357349
A document-centric approach for developing the tolAPC ontology. PMID:29179777
FANTOM5 CAGE profiles of human and mouse samples. PMID:28850106
FANTOM5 CAGE profiles of human and mouse reprocessed for GRCh38 and GRCm38 genome assemblies. PMID:28850105
A Children's Oncology Group and TARGET initiative exploring the genetic landscape of Wilms tumor. PMID:28825729
The Image Data Resource: A Bioimage Data Integration and Publication Platform. PMID:28775673
Listeriomics: an Interactive Web Platform for Systems Biology of Listeria. PMID:28317029
Measures for interoperability of phenotypic data: minimum information requirements and formatting. PMID:27843484
FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki. PMID:27402679
GEE: An Informatics Tool for Gene Expression Data Explore. PMID:27200217
The Ontology for Biomedical Investigations. PMID:27128319
Preparing Laboratory and Real-World EEG Data for Large-Scale Analysis: A Containerized Approach. PMID:27014048
Principles of metadata organization at the ENCODE data coordination center. PMID:26980513
An ISA-TAB-Nano based data collection framework to support data-driven modelling of nanotoxicology. PMID:26665069
A general concept for consistent documentation of computational analyses. PMID:26055099
SaDA: From Sampling to Data Analysis-An Extensible Open Source Infrastructure for Rapid, Robust and Automated Management and Analysis of Modern Ecological High-Throughput Microarray Data. PMID:26047146
The role of markup for enabling interoperability in health informatics. PMID:26042043
The species translation challenge-a systems biology perspective on human and rat bronchial epithelial cells. PMID:25977767
Intuitive web-based experimental design for high-throughput biomedical data. PMID:25954760
Development of data representation standards by the human proteome organization proteomics standards initiative. PMID:25726569
Gateways to the FANTOM5 promoter level mammalian expression atlas. PMID:25723102
Semantically linking in silico cancer models. PMID:25520553
linkedISA: semantic representation of ISA-Tab experimental metadata. PMID:25472428
Simulation environment and graphical visualization environment: a COPD use-case. PMID:25471327
Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data. PMID:25414366
Fingerprints of a message: integrating positional information on the transcriptome. PMID:25364746
ArrayExpress update--simplifying data submissions. PMID:25361974
GlycoPattern: a web platform for glycan array mining. PMID:25143288
CSEO - the Cigarette Smoke Exposure Ontology. PMID:25093069
A digital repository with an extensible data model for biobanking and genomic analysis management. PMID:25077808
The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience. PMID:24980485
The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again. PMID:24564732
MaTSE: the gene expression time-series explorer. PMID:24564291
Systems toxicology: from basic research to risk assessment. PMID:24446777
Semantic integration of gene expression analysis tools and data sources using software connectors. PMID:24341380
Biomarkers in autism spectrum disorder: the old and the new. PMID:24096533
Metadata management and semantics in microarray repositories. PMID:24052712
Transcriptional profiling of Zea mays roots reveals roles for jasmonic acid and terpenoids in resistance against Phytophthora cinnamomi. PMID:23430324
XperimentR: painless annotation of a biological experiment for the laboratory scientist. PMID:23323856
ISA-TAB-Nano: a specification for sharing nanomaterial research data in spreadsheet-based format. PMID:23311978
Overview of DNA microarrays: types, applications, and their future. PMID:23288464
Multiscale integration of -omic, imaging, and clinical data in biomedical informatics. PMID:23231990
ArrayExpress update--trends in database growth and links to data analysis tools. PMID:23193272
Data management strategies for multinational large-scale systems biology projects. PMID:23047157
VarioML framework for comprehensive variation data representation and exchange. PMID:23031277
BioGPS and GXD: mouse gene expression data-the benefits and challenges of data integration. PMID:22847375
MuteinDB: the mutein database linking substrates, products and enzymatic reactions directly with genetic variants of enzymes. PMID:22730453
MGEx-Udb: a mammalian uterus database for expression-based cataloguing of genes across conditions, including endometriosis and cervical cancer. PMID:22606288
graph2tab, a library to convert experimental workflow graphs into tabular formats. PMID:22556367
MageComet--web application for harmonizing existing large-scale experiment descriptions. PMID:22474121
Guidelines for information about therapy experiments: a proposal on best practice for recording experimental data on cancer therapy. PMID:22226027
The BioSample Database (BioSD) at the European Bioinformatics Institute. PMID:22096232
BμG@Sbase--a microbial gene expression and comparative genomic database. PMID:21948792
The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details. PMID:21856757
Informatics and standards for nanomedicine technology. PMID:21721140
Type VIII collagen modulates TGF-β1-induced proliferation of mesangial cells. PMID:21372207
Data standards for Omics data: the basis of data sharing and reuse. PMID:21370078
A pipeline for RNA-seq data processing and quality assessment. PMID:21233166
Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. PMID:21075797
ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments. PMID:21071405
PathEx: a novel multi factors based datasets selector web tool. PMID:20969778
Gravitation field algorithm and its application in gene cluster. PMID:20854683
Exposing the cancer genome atlas as a SPARQL endpoint. PMID:20851208
Analyzing schizophrenia by DNA microarrays. PMID:20801428
Structured digital tables on the Semantic Web: toward a structured digital literature. PMID:20739925
Annotare--a tool for annotating high-throughput biomedical investigations and resulting data. PMID:20733062
ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. PMID:20679334
TabSQL: a MySQL tool to facilitate mapping user data to public databases. PMID:20573251
A quick guide to large-scale genomic data mining. PMID:20523745
Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data. PMID:20369061
XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments. PMID:20214801
An efficient algorithm for the stochastic simulation of the hybridization of DNA to microarrays. PMID:20003312
SimplevisGrid: grid services for visualization of diverse biomedical knowledge and molecular systems data. PMID:19964624
Data reporting standards: making the things we use better. PMID:19939294
BASE--2nd generation software for microarray data management and analysis. PMID:19822003
A System for Information Management in BioMedical Studies--SIMBioMS. PMID:19633095
Importing ArrayExpress datasets into R/Bioconductor. PMID:19505942
MIMAS 3.0 is a Multiomics Information Management and Annotation System. PMID:19450266
SDRF2GRAPH: a visualization tool of a spreadsheet-based description of experimental processes. PMID:19422683
Owner controlled data exchange in nutrigenomic collaborations: the NuGO information network. PMID:19408032
The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. PMID:19374775
MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB. PMID:19038988
ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression. PMID:19015125
MiMiR--an integrated platform for microarray data sharing, mining and analysis. PMID:18801157
Accessing and integrating data and knowledge for biomedical research. PMID:18660883
Data capture in bioinformatics: requirements and experiences with Pedro. PMID:18402673
A software framework for microarray and gene expression object model (MAGE-OM) array design annotation. PMID:18366695
Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). PMID:18327244
Ensembl 2008. PMID:18000006
CEBS--Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data. PMID:17962311
Meta-analysis of microarray results: challenges, opportunities, and recommendations for standardization. PMID:17651921
ArrayExpress--a public database of microarray experiments and gene expression profiles. PMID:17132828
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assay
metasource: Fairsharing.org
version: FAIRsharing.org: MAGE-TAB; MicroArray Gene Expression Tabular Format; DOI: https://doi.org/10.25504/FAIRsharing.ak8p5g; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
dna microarray
metasource: Fairsharing.org
version: FAIRsharing.org: MAGE-TAB; MicroArray Gene Expression Tabular Format; DOI: https://doi.org/10.25504/FAIRsharing.ak8p5g; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
report
metasource: Fairsharing.org
version: FAIRsharing.org: MAGE-TAB; MicroArray Gene Expression Tabular Format; DOI: https://doi.org/10.25504/FAIRsharing.ak8p5g; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Tags
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assay
metasource: Fairsharing.orgversion: FAIRsharing.org: MAGE-TAB; MicroArray Gene Expression Tabular Format; DOI: https://doi.org/10.25504/FAIRsharing.ak8p5g; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
dna microarray
metasource: Fairsharing.orgversion: FAIRsharing.org: MAGE-TAB; MicroArray Gene Expression Tabular Format; DOI: https://doi.org/10.25504/FAIRsharing.ak8p5g; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
report
metasource: Fairsharing.orgversion: FAIRsharing.org: MAGE-TAB; MicroArray Gene Expression Tabular Format; DOI: https://doi.org/10.25504/FAIRsharing.ak8p5g; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
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