ArticlePloS one2011
Functional analysis beyond enrichment: non-redundant reciprocal linkage of genes and biological terms.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
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- Gene-set Enrichment with Mathematical Biology (GEMB).GigaScience · 2020Article
- Genome-Wide Analysis Reveals Mucociliary Remodeling of the Nasal Airway Epithelium Induced by Urban PMAmerican journal of respiratory cell and molecular biology · 2020Article
- Exomes of Ductal Luminal Breast Cancer Patients from Southwest Colombia: Gene Mutational Profile and Related Expression Alterations.Biomolecules · 2020Article
- Deciphering Master Gene Regulators and Associated Networks of Human Mesenchymal Stromal Cells.Biomolecules · 2020Article
- Elevated COScientific reports · 2019Article
- Genes with human-specific features are primarily involved with brain, immune and metabolic evolution.BMC bioinformatics · 2019Article
- ASCT1 (Slc1a4) transporter is a physiologic regulator of brain d-serine and neurodevelopment.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Rare Disease Mechanisms Identified by Genealogical Proteomics of Copper Homeostasis Mutant Pedigrees.Cell systems · 2018Article
- CD4+CD28+KIR+CD11aJournal of autoimmunity · 2018Article
- Article
- Activated signature of antiphospholipid syndrome neutrophils reveals potential therapeutic target.JCI insight · 2017Article
- Monocyte-derived alveolar macrophages drive lung fibrosis and persist in the lung over the life span.The Journal of experimental medicine · 2017Article
- Identifying disease-associated pathways in one-phenotype data based on reversal gene expression orderings.Scientific reports · 2017Article
- Dysbindin Deficiency Modifies the Expression of GABA Neuron and Ion Permeation Transcripts in the Developing Hippocampus.Frontiers in genetics · 2017Article
- The Proteome of BLOC-1 Genetic Defects Identifies the Arp2/3 Actin Polymerization Complex to Function Downstream of the Schizophrenia Susceptibility Factor Dysbindin at the Synapse.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2016Article
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Functional analysis of large sets of genes and proteins is becoming more and more necessary with the increase of experimental biomolecular data at omic-scale. Enrichment analysis is by far the most popular available methodology to derive functional implications of sets of cooperating genes. The problem with these techniques relies in the redundancy of resulting information, that in most cases generate lots of trivial results with high risk to mask the reality of key biological events. We present and describe a computational method, called GeneTerm Linker, that filters and links enriched output data identifying sets of associated genes and terms, producing metagroups of coherent biological significance. The method uses fuzzy reciprocal linkage between genes and terms to unravel their functional convergence and associations. The algorithm is tested with a small set of well known interacting proteins from yeast and with a large collection of reference sets from three heterogeneous resources: multiprotein complexes (CORUM), cellular pathways (SGD) and human diseases (OMIM). Statistical Precision, Recall and balanced F-score are calculated showing robust results, even when different levels of random noise are included in the test sets. Although we could not find an equivalent method, we present a comparative analysis with a widely used method that combines enrichment and functional annotation clustering. A web application to use the method here proposed is provided at http://gtlinker.cnb.csic.es.
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