SynthesisBioinformatics (Oxford, England)2009
A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide.
Synthesis in Bioinformatics (Oxford, England), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers, 2 of them syntheses that pooled it.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
67 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- A data similarity-based strategy for meta-analysis of transcriptional profiles in cancer.PloS one · 2013Pooled it
- A novel tissue-specific meta-analysis approach for gene expression predictions, initiated with a mammalian gene expression testis database.BMC genomics · 2010Pooled it
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- BioVDB: biological vector database for high-throughput gene expression meta-analysis.Frontiers in artificial intelligence · 2024Article
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- A Bioinformatics Perspective on the Links Between Tetraspanin-Enriched Microdomains and Cardiovascular Pathophysiology.Frontiers in cardiovascular medicine · 2021Article
- CSAG1 maintains the integrity of the mitotic centrosome in cells with defective p53.Journal of cell science · 2020Article
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- The long noncoding RNAScience advances · 2019Article
- Comparative Analysis of Developmental Transcriptome Maps of Arabidopsis thaliana and Solanum lycopersicum.Genes · 2019Article
- Characterization of cxorf21 Provides Molecular Insight Into Female-Bias Immune Response in SLE Pathogenesis.Frontiers in immunology · 2019Article
- Targeting ELTD1, an angiogenesis marker for glioblastoma (GBM), also affects VEGFR2: molecular-targeted MRI assessment.American journal of nuclear medicine and molecular imaging · 2019Article
- Interpretation of an individual functional genomics experiment guided by massive public data.Nature methods · 2018Article
- Tetraspanin-enriched microdomains regulate digitation junctions.Cellular and molecular life sciences : CMLS · 2018Article
- Consensus Coexpression Network Analysis Identifies Key Regulators of Flower and Fruit Development in Wild Strawberry.Plant physiology · 2018Article
7 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
Abstract
motivationApproximately 9334 (37%) of human genes have no publications documenting their function and, for those that are published, the number of publications per gene is highly skewed. Furthermore, for reasons not clear, the entry of new gene names into the literature has slowed in recent years. If we are to better understand human/mammalian biology and complete the catalog of human gene function, it is important to finish predicting putative functions for these genes based upon existing experimental evidence.
resultsA global meta-analysis (GMA) of all publicly available GEO two-channel human microarray datasets (3551 experiments total) was conducted to identify genes with recurrent, reproducible patterns of co-regulation across different conditions. Patterns of co-expression were divided into parallel (i.e. genes are up and down-regulated together) and anti-parallel. Several ranking methods to predict a gene's function based on its top 20 co-expressed gene pairs were compared. In the best method, 34% of predicted Gene Ontology (GO) categories matched exactly with the known GO categories for approximately 5000 genes analyzed versus only 3% for random gene sets. Only 2.4% of co-expressed gene pairs were found as co-occurring gene pairs in MEDLINE.
conclusionsVia a GO enrichment analysis, genes co-expressed in parallel with the query gene were frequently associated with the same GO categories, whereas anti-parallel genes were not. Combining parallel and anti-parallel genes for analysis resulted in fewer significant GO categories, suggesting they are best analyzed separately. Expression databases contain much unexpected genetic knowledge that has not yet been reported in the literature. A total of 1642 Human genes with unknown function were differentially expressed in at least 30 experiments. AVAILABILITY: Data matrix available upon request.
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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.