ArticleBioinformatics (Oxford, England)2015
ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
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- Single Cell Analysis of Peripheral TB-Associated Granulomatous Lymphadenitis.bioRxiv : the preprint server for biology · 2024Article
- A robust immune-related gene pairs signature for predicting the overall survival of esophageal cancer.BMC genomics · 2023Article
- Identification and validation of an immune-related gene pairs signature for three urologic cancers.Aging · 2022Article
- SARS-CoV-2 early infection signature identified potential key infection mechanisms and drug targets.BMC genomics · 2021Article
- Comparing tuberculosis gene signatures in malnourished individuals using the TBSignatureProfiler.BMC infectious diseases · 2021Article
- Drug vector representation: a tool for drug similarity analysis.Molecular genetics and genomics : MGG · 2020Article
- Glucocorticoids rapidly activate cAMP production via GFASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2020Article
- Pathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypes.BMC cancer · 2019Article
- Host and microbiome multi-omics integration: applications and methodologies.Biophysical reviews · 2019Review
- CaDrA: A Computational Framework for Performing Candidate Driver Analyses Using Genomic Features.Frontiers in genetics · 2019Article
- Functional and genomic analyses reveal therapeutic potential of targeting β-catenin/CBP activity in head and neck cancer.Genome medicine · 2018Article
- Alternative empirical Bayes models for adjusting for batch effects in genomic studies.BMC bioinformatics · 2018Article
- Glutamine-utilizing transaminases are a metabolic vulnerability of TAZ/YAP-activated cancer cells.EMBO reports · 2018Article
- Combating subclonal evolution of resistant cancer phenotypes.Nature communications · 2017Article
- Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes.Genome medicine · 2017Article
- Intracellular and intercellular signaling networks in cancer initiation, development and precision anti-cancer therapy: RAS acts as contextual signaling hub.Seminars in cell & developmental biology · 2016Review
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9 authors.
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Abstract
motivationAlthough gene-expression signature-based biomarkers are often developed for clinical diagnosis, many promising signatures fail to replicate during validation. One major challenge is that biological samples used to generate and validate the signature are often from heterogeneous biological contexts-controlled or in vitro samples may be used to generate the signature, but patient samples may be used for validation. In addition, systematic technical biases from multiple genome-profiling platforms often mask true biological variation. Addressing such challenges will enable us to better elucidate disease mechanisms and provide improved guidance for personalized therapeutics.
resultsHere, we present a pathway profiling toolkit, Adaptive Signature Selection and InteGratioN (ASSIGN), which enables robust and context-specific pathway analyses by efficiently capturing pathway activity in heterogeneous sets of samples and across profiling technologies. The ASSIGN framework is based on a flexible Bayesian factor analysis approach that allows for simultaneous profiling of multiple correlated pathways and for the adaptation of pathway signatures into specific disease. We demonstrate the robustness and versatility of ASSIGN in estimating pathway activity in simulated data, cell lines perturbed pathways and in primary tissues samples including The Cancer Genome Atlas breast carcinoma samples and liver samples exposed to genotoxic carcinogens. AVAILABILITY AND IMPLEMENTATION: Software for our approach is available for download at: http://www.bioconductor.org/packages/release/bioc/html/ASSIGN.html and https://github.com/wevanjohnson/ASSIGN.
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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.