ArticleBioinformatics (Oxford, England)2009
LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data.
Article 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 122 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
122 citing papers in PubMed.
- Metreleptin therapy for nonalcoholic steatohepatitis: Open-label therapy interventions in two different clinical settings.Med (New York, N.Y.) · 2021Trial
- Identification of factors associated with sural nerve regeneration and degeneration in diabetic neuropathy.Diabetes care · 2013Trial
- Skeletal muscle gene expression in response to resistance exercise: sex specific regulation.BMC genomics · 2010Trial
- DEDUCE: statistical inference on disease-associated genes uncovers tissue-disease associations.NAR genomics and bioinformatics · 2025Article
- Perinatal Lead (Pb) Exposure Increases Mouse Embryonic Weight and Alters Neuronal Gene Expression.bioRxiv : the preprint server for biology · 2025Article
- Current approaches and outstanding challenges of functional annotation of metabolites: a comprehensive review.Briefings in bioinformatics · 2024Review
- danRerLib: a Python package for zebrafish transcriptomics.Bioinformatics advances · 2024Article
- GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership.Genome biology · 2023Article
- GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership.bioRxiv : the preprint server for biology · 2023Article
- Coherent pathway enrichment estimation by modeling inter-pathway dependencies using regularized regression.Bioinformatics (Oxford, England) · 2023Article
- Perinatal Lead Exposure Promotes Sex-Specific Epigenetic Programming of Disease-Relevant Pathways in Mouse Heart.Toxics · 2023Article
- Article
- Molecular differences in brain regional vulnerability to aging between males and females.Frontiers in aging neuroscience · 2023Article
- Navigating Transcriptomic Connectivity Mapping Workflows to Link Chemicals with Bioactivities.Chemical research in toxicology · 2022Review
- Determining biomarkers for evaluation and diagnosis of hereditary angioedema.Clinical and translational allergy · 2022Article
- Applied Machine Learning in Industry 4.0: Case-Study Research in Predictive Models for Black Carbon Emissions.Sensors (Basel, Switzerland) · 2022Article
- LRcell: detecting the source of differential expression at the sub-cell-type level from bulk RNA-seq data.Briefings in bioinformatics · 2022Article
- Three dimensional modeling of biologically relevant fluid shear stress in human renal tubule cells mimics in vivo transcriptional profiles.Scientific reports · 2021Article
- Detection of Genes inGenes · 2021Article
- Genetic and epigenetic changes in the eutopic endometrium of women with endometriosis: association with decreased endometrial αvβ3 integrin expression.Molecular human reproduction · 2021Article
62 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
3 authors.
Funding
Abstract
motivationThe elucidation of biological pathways enriched with differentially expressed genes has become an integral part of the analysis and interpretation of microarray data. Several statistical methods are commonly used in this context, but the question of the optimal approach has still not been resolved.
resultsWe present a logistic regression-based method (LRpath) for identifying predefined sets of biologically related genes enriched with (or depleted of) differentially expressed transcripts in microarray experiments. We functionally relate the odds of gene set membership with the significance of differential expression, and calculate adjusted P-values as a measure of statistical significance. The new approach is compared with Fisher's exact test and other relevant methods in a simulation study and in the analysis of two breast cancer datasets. Overall results were concordant between the simulation study and the experimental data analysis, and provide useful information to investigators seeking to choose the appropriate method. LRpath displayed robust behavior and improved statistical power compared with tested alternatives. It is applicable in experiments involving two or more sample types, and accepts significance statistics of the investigator's choice as input.
Indexed as
Identifiers
What OpenQuestion holds
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.