ArticleFrontiers in neuroscience2011
Exploiting Statistical Methodologies and Controlled Vocabularies for Prioritized Functional Analysis of Genomic Experiments: the StRAnGER Web Application.
Article in Frontiers in neuroscience, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers, 2 of them syntheses that pooled it.
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13 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Comparative Meta-Analysis of Transcriptomics Data during Cellular Senescence and In Vivo Tissue Ageing.Oxidative medicine and cellular longevity · 2015Pooled it
- A comparative genomic study in schizophrenic and in bipolar disorder patients, based on microarray expression profiling meta-analysis.TheScientificWorldJournal · 2013Pooled it
- Control of anterior GRadient 2 (AGR2) dimerization links endoplasmic reticulum proteostasis to inflammation.EMBO molecular medicine · 2019Article
- A Computational Pipeline for the Extraction of Actionable Biological Information From NGS-Phage Display Experiments.Frontiers in physiology · 2019Article
- ANASTASIA: An Automated Metagenomic Analysis Pipeline for Novel Enzyme Discovery Exploiting Next Generation Sequencing Data.Frontiers in genetics · 2019Article
- Article
- GRYFUN: a web application for GO term annotation visualization and analysis in protein sets.PloS one · 2015Article
- KENeV: A web-application for the automated reconstruction and visualization of the enriched metabolic and signaling super-pathways deriving from genomic experiments.Computational and structural biotechnology journal · 2015Article
- Bioinformatic analysis reveals a pattern of STAT3-associated gene expression specific to basal-like breast cancers in human tumors.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Article
- HuR-regulated mRNAs associated with nuclear hnRNP A1-RNP complexes.International journal of molecular sciences · 2013Article
- The KUPNetViz: a biological network viewer for multiple -omics datasets in kidney diseases.BMC bioinformatics · 2013Article
- Application of an integrative computational framework in trancriptomic data of atherosclerotic mice suggests numerous molecular players.Advances in bioinformatics · 2012Article
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Abstract
StRAnGER is a web application for the automated statistical analysis of annotated gene profiling experiments, exploiting controlled biological vocabularies, like the Gene Ontology or the KEGG pathways terms. Starting from annotated lists of differentially expressed genes and gene enrichment scores, regarding the terms of each vocabulary, StRAnGER repartitions and reorders the initial distribution of terms to define a new distribution of elements. Each element pools terms holding the same enrichment score. The new distribution thus derived, is reordered in a decreasing order to the right, according to the observation score of the elements, while elements with the same score, are sorted again in a decreasing order of their enrichment scores. By applying bootstrapping techniques, a corrected measure of the statistical significance of these elements is derived, which enables the selection of terms mapped to these elements, unambiguously associated with respective significant gene sets. The selected terms are immunized against the bias infiltrating statistical enrichment analyses, producing technically very high statistical scores, due to the finite nature of the data population. Besides their high statistical score, another selection criterion for the terms is the number of their members, something that incurs a biological prioritization in line with a Systems Biology context. The output derived, represents a detailed ranked list of significant terms, which constitute a starting point for further functional analysis.
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