ArticleThe pharmacogenomics journal2010
Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes.
Article in The pharmacogenomics journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed.
- Prebiotic proanthocyanidins inhibit bile reflux-induced esophageal adenocarcinoma through reshaping the gut microbiome and esophageal metabolome.JCI insight · 2024Article
- The use of evidence from high-throughput screening and transcriptomic data in human health risk assessments.Toxicology and applied pharmacology · 2019Article
- Platform-independent gene expression signature differentiates sessile serrated adenomas/polyps and hyperplastic polyps of the colon.BMC medical genomics · 2017Article
- Evidence for the importance of post-transcriptional regulatory changes in ovarian cancer progression and the contribution of miRNAs.Scientific reports · 2017Article
- A Cell-Surface Membrane Protein Signature for Glioblastoma.Cell systems · 2017Article
- Acquired resistance of pancreatic cancer cells to cisplatin is multifactorial with cell context-dependent involvement of resistance genes.Cancer gene therapy · 2016Article
- Protein Interaction Networks Link Schizophrenia Risk Loci to Synaptic Function.Schizophrenia bulletin · 2016Article
- The FDA's Experience with Emerging Genomics Technologies-Past, Present, and Future.The AAPS journal · 2016Review
- Article
- Feasibility of implementing molecular-guided therapy for the treatment of patients with relapsed or refractory neuroblastoma.Cancer medicine · 2015Article
- Reconstitution of the ERG Gene Expression Network Reveals New Biomarkers and Therapeutic Targets in ERG Positive Prostate Tumors.Journal of Cancer · 2015Article
- A testing strategy to predict risk for drug-induced liver injury in humans using high-content screen assays and the 'rule-of-two' model.Archives of toxicology · 2014Article
- A model of early human embryonic stem cell differentiation reveals inter- and intracellular changes on transition to squamous epithelium.Stem cells and development · 2012Article
- Article
- Algebraic comparison of partial lists in bioinformatics.PloS one · 2012Article
- Quality assurance of RNA expression profiling in clinical laboratories.The Journal of molecular diagnostics : JMD · 2012Review
- The influence of feature selection methods on accuracy, stability and interpretability of molecular signatures.PloS one · 2011Article
- Clinical implementation of RNA signatures for pharmacogenomic decision-making.Pharmacogenomics and personalized medicine · 2011Article
- The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.Nature biotechnology · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
22 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene expression signatures of toxicity and clinical response benefit both safety assessment and clinical practice; however, difficulties in connecting signature genes with the predicted end points have limited their application. The Microarray Quality Control Consortium II (MAQCII) project generated 262 signatures for ten clinical and three toxicological end points from six gene expression data sets, an unprecedented collection of diverse signatures that has permitted a wide-ranging analysis on the nature of such predictive models. A comprehensive analysis of the genes of these signatures and their nonredundant unions using ontology enrichment, biological network building and interactome connectivity analyses demonstrated the link between gene signatures and the biological basis of their predictive power. Different signatures for a given end point were more similar at the level of biological properties and transcriptional control than at the gene level. Signatures tended to be enriched in function and pathway in an end point and model-specific manner, and showed a topological bias for incoming interactions. Importantly, the level of biological similarity between different signatures for a given end point correlated positively with the accuracy of the signature predictions. These findings will aid the understanding, and application of predictive genomic signatures, and support their broader application in predictive medicine.
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.