Cargando…

Enhancing Interpretability of Gene Signatures with Prior Biological Knowledge

Biological interpretability is a key requirement for the output of microarray data analysis pipelines. The most used pipeline first identifies a gene signature from the acquired measurements and then uses gene enrichment analysis as a tool for functionally characterizing the obtained results. Recent...

Descripción completa

Detalles Bibliográficos
Autores principales:	Squillario, Margherita, Barbieri, Matteo, Verri, Alessandro, Barla, Annalisa
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	MDPI 2016
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5003491/ https://www.ncbi.nlm.nih.gov/pubmed/27600081 http://dx.doi.org/10.3390/microarrays5020015

Ejemplares similares

Knowledge Driven Variable Selection (KDVS) – a new approach to enrichment analysis of gene signatures obtained from high–throughput data
por: Zycinski, Grzegorz, et al.
Publicado: (2013)

A computational procedure for functional characterization of potential marker genes from molecular data: Alzheimer's as a case study
por: Squillario, Margherita, et al.
Publicado: (2011)

A telescope GWAS analysis strategy, based on SNPs-genes-pathways ensamble and on multivariate algorithms, to characterize late onset Alzheimer’s disease
por: Squillario, Margherita, et al.
Publicado: (2020)

New miRNA Signature Heralds Human NK Cell Subsets at Different Maturation Steps: Involvement of miR-146a-5p in the Regulation of KIR Expression
por: Pesce, Silvia, et al.
Publicado: (2018)

A biology-driven approach identifies the hypoxia gene signature as a predictor of the outcome of neuroblastoma patients
por: Fardin, Paolo, et al.
Publicado: (2010)

The l(1)-l(2 )regularization framework unmasks the hypoxia signature hidden in the transcriptome of a set of heterogeneous neuroblastoma cell lines
por: Fardin, Paolo, et al.
Publicado: (2009)

Transplantation Induces Profound Changes in the Transcriptional Asset of Hematopoietic Stem Cells: Identification of Specific Signatures Using Machine Learning Techniques
por: Cilloni, Daniela, et al.
Publicado: (2020)

Effect of Size and Heterogeneity of Samples on Biomarker Discovery: Synthetic and Real Data Assessment
por: Di Camillo, Barbara, et al.
Publicado: (2012)

Identification of Multiple Hypoxia Signatures in Neuroblastoma Cell Lines by l(1)-l(2) Regularization and Data Reduction
por: Fardin, Paolo, et al.
Publicado: (2010)

Genome instability model of metastatic neuroblastoma tumorigenesis by a dictionary learning algorithm
por: Masecchia, Salvatore, et al.
Publicado: (2015)

Prognostic gene signatures for patient stratification in breast cancer - accuracy, stability and interpretability of gene selection approaches using prior knowledge on protein-protein interactions
por: Cun, Yupeng, et al.
Publicado: (2012)

Gene Network Reconstruction by Integration of Prior Biological Knowledge
por: Li, Yupeng, et al.
Publicado: (2015)

Interpretation Training Influences Memory for Prior Interpretations
por: Salemink, Elske, et al.
Publicado: (2010)

Incorporating biological prior knowledge for Bayesian learning via maximal knowledge-driven information priors
por: Boluki, Shahin, et al.
Publicado: (2017)

The hidden information in patient-reported outcomes and clinician-assessed outcomes: multiple sclerosis as a proof of concept of a machine learning approach
por: Brichetto, Giampaolo, et al.
Publicado: (2019)

The Importance of Biologic Knowledge and Gene Expression Context for Genomic Data Interpretation
por: Zimmermann, Michael T.
Publicado: (2018)

Chapter 8: Biological Knowledge Assembly and Interpretation
por: Kim, Ju Han
Publicado: (2012)

Quantitative utilization of prior biological knowledge in the Bayesian network modeling of gene expression data
por: Gao, Shouguo, et al.
Publicado: (2011)

Different Features of Tumor-Associated NK Cells in Patients With Low-Grade or High-Grade Peritoneal Carcinomatosis
por: Pesce, Silvia, et al.
Publicado: (2019)

Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology
por: Lovering, Ruth C., et al.
Publicado: (2018)

Reconstruction of gene networks using prior knowledge
por: Ghanbari, Mahsa, et al.
Publicado: (2015)

signatureSearch: environment for gene expression signature searching and functional interpretation
por: Duan, Yuzhu, et al.
Publicado: (2020)

The structure of prior knowledge enhances memory in experts by reducing interference
por: Wing, Erik A., et al.
Publicado: (2022)

Integrating educational knowledge: reactivation of prior knowledge during educational learning enhances memory integration
por: van Kesteren, Marlieke Tina Renée, et al.
Publicado: (2018)

Updating Urinary Microbiome Analyses to Enhance Biologic Interpretation
por: Siddiqui, Nazema Y., et al.
Publicado: (2022)

Bayesian network prior: network analysis of biological data using external knowledge
por: Isci, Senol, et al.
Publicado: (2014)

Exploiting prior knowledge about biological macromolecules in cryo-EM structure determination
por: Kimanius, Dari, et al.
Publicado: (2021)

Incorporating prior biological knowledge for network-based differential gene expression analysis using differentially weighted graphical LASSO
por: Zuo, Yiming, et al.
Publicado: (2017)

Diagenetic and Biological Overprints in Geochemical Signatures of the Gigantoproductus Tertiary Layer (Brachiopoda): Assessing the Paleoclimatic Interpretation
por: Mateos-Carralafuente, José R., et al.
Publicado: (2023)

Semantic Signature: Comparative Interpretation of Gene Expression on a Semantic Space
por: Kim, Jihun, et al.
Publicado: (2016)

Boolean network inference from time series data incorporating prior biological knowledge
por: Haider, Saad, et al.
Publicado: (2012)

Prior Biological Knowledge Improves Genomic Prediction of Growth-Related Traits in Arabidopsis thaliana
por: Farooq, Muhammad, et al.
Publicado: (2021)

Interpreting vision and language generative models with semantic visual priors
por: Cafagna, Michele, et al.
Publicado: (2023)

Prior knowledge guided eQTL mapping for identifying candidate genes
por: Wang, Yunli, et al.
Publicado: (2016)

Integration of gene expression data with prior knowledge for network analysis and validation
por: Ante, Michael, et al.
Publicado: (2011)

Identifying Genes Involved in Cyclic Processes by Combining Gene Expression Analysis and Prior Knowledge
por: Zhao, Wentao, et al.
Publicado: (2009)

Characterization of the Effectiveness of Reporting Lists of Small Feature Sets Relative to the Accuracy of the Prior Biological Knowledge
por: Zhao, Chen, et al.
Publicado: (2010)

Relevance of different prior knowledge sources for inferring gene interaction networks
por: Olsen, Catharina, et al.
Publicado: (2014)

Prior knowledge driven Granger causality analysis on gene regulatory network discovery
por: Yao, Shun, et al.
Publicado: (2015)

Learning interpretable cellular and gene signature embeddings from single-cell transcriptomic data
por: Zhao, Yifan, et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_3oef4q66j92fvoqr0u1klin0d4