ArticleNPJ systems biology and applications2018
Classification of gene signatures for their information value and functional redundancy.
Article in NPJ systems biology and applications, 2018. 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.
- Interpretable and scalable spatial gene set activity analysis with GESSO uncovers functional tissue architecture.bioRxiv : the preprint server for biology · 2026Article
- Geometric multidimensional representation of omic signatures.Frontiers in bioinformatics · 2026Article
- adverSCarial: assessing the vulnerability of single-cell RNA-sequencing classifiers to adversarial attacks.Bioinformatics (Oxford, England) · 2025Article
- SignalingProfiler 2.0 a network-based approach to bridge multi-omics data to phenotypic hallmarks.NPJ systems biology and applications · 2024Article
- PMHeliyon · 2024Article
- ssMutPA: single-sample mutation-based pathway analysis approach for cancer precision medicine.GigaScience · 2024Article
- Pan-cancer onco-signatures reveal a novel mitochondrial subtype of luminal breast cancer with specific regulators.Journal of translational medicine · 2023Article
- Application of perturbation gene expression profiles in drug discovery-From mechanism of action to quantitative modelling.Frontiers in systems biology · 2023Review
- Optimized Transcriptional Signature for Evaluation of MEK/ERK Pathway Baseline Activity and Long-Term Modulations in Ovarian Cancer.International journal of molecular sciences · 2022Article
- Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment.Nature genetics · 2022Article
- Development of a miRNA-based classifier for detection of colorectal cancer molecular subtypes.Molecular oncology · 2022Article
- hacksig: a unified and tidy R framework to easily compute gene expression signature scores.Bioinformatics (Oxford, England) · 2022Article
- Radiotherapy resistance: identifying universal biomarkers for various human cancers.Journal of cancer research and clinical oncology · 2022Review
- Osteoarthritis Data Integration Portal (OsteoDIP): A web-based gene and non-coding RNA expression database.Osteoarthritis and cartilage open · 2022Article
- Construction and validation of a novel gene signature for predicting the prognosis of osteosarcoma.Scientific reports · 2022Article
- Pan-cancer analysis of pathway-based gene expression pattern at the individual level reveals biomarkers of clinical prognosis.Cell reports methods · 2021Article
- Derivation and Application of Molecular Signatures to Prostate Cancer: Opportunities and Challenges.Cancers · 2021Review
- Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses.Molecular systems biology · 2021Article
- signatureSearch: environment for gene expression signature searching and functional interpretation.Nucleic acids research · 2020Article
- SPEED2: inferring upstream pathway activity from differential gene expression.Nucleic acids research · 2020Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene signatures are more and more used to interpret results of omics data analyses but suffer from compositional (large overlap) and functional (correlated read-outs) redundancy. Moreover, many gene signatures rarely come out as significant in statistical tests. Based on pan-cancer data analysis, we construct a restricted set of 962 signatures defined as informative and demonstrate that they have a higher probability to appear enriched in comparative cancer studies. We show that the majority of informative signatures conserve their weights for the genes composing the signature (eigengenes) from one cancer type to another. We finally construct InfoSigMap, an interactive online map of these signatures and their cross-correlations. This map highlights the structure of compositional and functional redundancies between informative signatures, and it charts the territories of biological functions. InfoSigMap can be used to visualize the results of omics data analyses and suggests a rearrangement of existing gene sets.
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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.