ArticleScientific data2017
Precision annotation of digital samples in NCBI's gene expression omnibus.
Article in Scientific data, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers, 5 of them syntheses that pooled it.
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Who cites it
26 citing papers in PubMed, 5 syntheses or guidelines pooled it.
- Human Transcriptomic Meta-Analysis Identifies Immune-Redox Remodeling and Impaired Vascular Wall Homeostasis in Abdominal Aortic Aneurysm.International journal of molecular sciences · 2026Pooled it
- Metaanalysis Reveals Genetic Correlates of Osteoporosis Pathogenesis.The Journal of rheumatology · 2021Pooled it
- Meta-Analysis Reveals the Prognostic Relevance of Nuclear and Membrane-Associated Bile Acid Receptors in Gastric Cancer.Clinical and translational gastroenterology · 2021Pooled it
- Pooled it
- Critical period plasticity-related transcriptional aberrations in schizophrenia and bipolar disorder.Schizophrenia research · 2019Pooled it
- Genetic Profiling of Primary Versus Metastatic Ewing Sarcoma for Therapeutic Target Identification.Life (Basel, Switzerland) · 2026Article
- Using semantic search to find publicly available gene-expression datasets.Bioinformatics (Oxford, England) · 2026Article
- Integrated analysis of hub genes and intrinsically disordered regions in triple-negative breast cancer.Journal, genetic engineering & biotechnology · 2024Article
- TidyGEO: preparing analysis-ready datasets from Gene Expression Omnibus.Journal of integrative bioinformatics · 2024Article
- Standigm ASK™: knowledge graph and artificial intelligence platform applied to target discovery in idiopathic pulmonary fibrosis.Briefings in bioinformatics · 2024Article
- The role of machine learning in advancing diabetic foot: a review.Frontiers in endocrinology · 2024Review
- Article
- Systematic tissue annotations of genomics samples by modeling unstructured metadata.Nature communications · 2022Article
- Dissecting novel mechanisms of hepatitis B virus related hepatocellular carcinoma using meta-analysis of public data.World journal of gastrointestinal oncology · 2022Article
- Transcriptome changes in stages of non-alcoholic fatty liver disease.World journal of hepatology · 2022Article
- GeMI: interactive interface for transformer-based Genomic Metadata Integration.Database : the journal of biological databases and curation · 2022Article
- An integrated analysis of prognostic and immune infiltrates for hub genes as potential survival indicators in patients with lung adenocarcinoma.World journal of surgical oncology · 2022Article
- Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.Genome biology · 2022Article
- Probing predilection to Crohn's disease and Crohn's disease flares: A crowd-sourced bioinformatics approach.Journal of pathology informatics · 2022Article
- A merged microarray meta-dataset for transcriptionally profiling colorectal neoplasm formation and progression.Scientific data · 2021Article
Corrections and comments
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Authors and funding
19 authors.
Funding
Abstract
The Gene Expression Omnibus (GEO) contains more than two million digital samples from functional genomics experiments amassed over almost two decades. However, individual sample meta-data remains poorly described by unstructured free text attributes preventing its largescale reanalysis. We introduce the Search Tag Analyze Resource for GEO as a web application (http://STARGEO.org) to curate better annotations of sample phenotypes uniformly across different studies, and to use these sample annotations to define robust genomic signatures of disease pathology by meta-analysis. In this paper, we target a small group of biomedical graduate students to show rapid crowd-curation of precise sample annotations across all phenotypes, and we demonstrate the biological validity of these crowd-curated annotations for breast cancer. STARGEO.org makes GEO data findable, accessible, interoperable and reusable (i.e., FAIR) to ultimately facilitate knowledge discovery. Our work demonstrates the utility of crowd-curation and interpretation of open 'big data' under FAIR principles as a first step towards realizing an ideal paradigm of precision medicine.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.