ArticleBMC research notes2012
Human gene correlation analysis (HGCA): a tool for the identification of transcriptionally co-expressed genes.
Article in BMC research notes, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Transcriptome and gene co-expression network analysis revealed a putative regulatory mechanism of low nitrogen response in rice seedlings.Frontiers in plant science · 2025Article
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- Density-based detection of cell transition states to construct disparate and bifurcating trajectories.Nucleic acids research · 2022Article
- Approaches in Gene Coexpression Analysis in Eukaryotes.Biology · 2022Review
- Analysis of ROQUIN, Tristetraprolin (TTP), and BDNF/miR-16/TTP regulatory axis in late onset Alzheimer's disease.Frontiers in aging neuroscience · 2022Article
- Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review.Biomolecules · 2021Review
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- MyoMiner: explore gene co-expression in normal and pathological muscle.BMC medical genomics · 2020Article
- A Deep Learning Approach Validates Genetic Risk Factors for Late Toxicity After Prostate Cancer Radiotherapy in a REQUITE Multi-National Cohort.Frontiers in oncology · 2020Article
- Precision Lasso: accounting for correlations and linear dependencies in high-dimensional genomic data.Bioinformatics (Oxford, England) · 2019Article
- Integration of Machine Learning Methods to Dissect Genetically Imputed Transcriptomic Profiles in Alzheimer's Disease.Frontiers in genetics · 2019Article
- Reconstruction and inference of the Lactococcus lactis MG1363 gene co-expression network.PloS one · 2019Article
- Dynamic sporulation gene co-expression networks for Bacillus subtilis 168 and the food-borne isolate Bacillus amyloliquefaciens: a transcriptomic model.Microbial genomics · 2018Article
- Parkinson's disease-associated genetic variation is linked to quantitative expression of inflammatory genes.PloS one · 2017Article
- Cogena, a novel tool for co-expressed gene-set enrichment analysis, applied to drug repositioning and drug mode of action discovery.BMC genomics · 2016Article
- Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- CellWhere: graphical display of interaction networks organized on subcellular localizations.Nucleic acids research · 2015Article
- ImmuCo: a database of gene co-expression in immune cells.Nucleic acids research · 2015Article
- MIrExpress: A Database for Gene Coexpression Correlation in Immune Cells Based on Mutual Information and Pearson Correlation.Journal of immunology research · 2015Article
- Coregulation of host-response genes in integument: switchover of gene expression correlation pattern and impaired immune responses induced by dipteran parasite infection in the silkworm, Bombyx mori.Journal of applied genetics · 2014Article
Corrections and comments
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7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBioinformatics and high-throughput technologies such as microarray studies allow the measure of the expression levels of large numbers of genes simultaneously, thus helping us to understand the molecular mechanisms of various biological processes in a cell.
findingsWe calculate the Pearson Correlation Coefficient (r-value) between probe set signal values from Affymetrix Human Genome Microarray samples and cluster the human genes according to the r-value correlation matrix using the Neighbour Joining (NJ) clustering method. A hyper-geometric distribution is applied on the text annotations of the probe sets to quantify the term overrepresentations. The aim of the tool is the identification of closely correlated genes for a given gene of interest and/or the prediction of its biological function, which is based on the annotations of the respective gene cluster.
conclusionHuman Gene Correlation Analysis (HGCA) is a tool to classify human genes according to their coexpression levels and to identify overrepresented annotation terms in correlated gene groups. It is available at: http://biobank-informatics.bioacademy.gr/coexpression/.
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