Cargando…

Effects of subsampling on characteristics of RNA-seq data from triple-negative breast cancer patients

BACKGROUND: Data from RNA-seq experiments provide a wealth of information about the transcriptome of an organism. However, the analysis of such data is very demanding. In this study, we aimed to establish robust analysis procedures that can be used in clinical practice. METHODS: We studied RNA-seq d...

Descripción completa

Detalles Bibliográficos
Autores principales:	Stupnikov, Alexey, Glazko, Galina V, Emmert-Streib, Frank
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2015
Materias:	Original Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4593382/ https://www.ncbi.nlm.nih.gov/pubmed/26253000 http://dx.doi.org/10.1186/s40880-015-0040-8

Ejemplares similares

Comparative evaluation of gene set analysis approaches for RNA-Seq data
por: Rahmatallah, Yasir, et al.
Publicado: (2014)

Comparing biological information contained in mRNA and non-coding RNAs for classification of lung cancer patients
por: Smolander, Johannes, et al.
Publicado: (2019)

Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline
por: Rahmatallah, Yasir, et al.
Publicado: (2016)

Pathway Analysis of Expression Data: Deciphering Functional Building Blocks of Complex Diseases
por: Emmert-Streib, Frank, et al.
Publicado: (2011)

Ensuring the statistical soundness of competitive gene set approaches: gene filtering and genome-scale coverage are essential
por: Tripathi, Shailesh, et al.
Publicado: (2013)

Gene Sets Net Correlations Analysis (GSNCA): a multivariate differential coexpression test for gene sets
por: Rahmatallah, Yasir, et al.
Publicado: (2014)

Statistical Inference and Reverse Engineering of Gene Regulatory Networks from Observational Expression Data
por: Emmert-Streib, Frank, et al.
Publicado: (2012)

GSAR: Bioconductor package for Gene Set analysis in R
por: Rahmatallah, Yasir, et al.
Publicado: (2017)

A Bayesian analysis of the chromosome architecture of human disorders by integrating reductionist data
por: Emmert-Streib, Frank, et al.
Publicado: (2012)

Prognostic gene expression signatures of breast cancer are lacking a sensible biological meaning
por: Manjang, Kalifa, et al.
Publicado: (2021)

Proteome-transcriptome alignment of molecular portraits achieved by self-contained gene set analysis: Consensus colon cancer subtypes case study
por: Glazko, Galina, et al.
Publicado: (2019)

Prostate Cancer Gene Regulatory Network Inferred from RNA-Seq Data
por: Moore, Daniel, et al.
Publicado: (2019)

Robustness of differential gene expression analysis of RNA-seq
por: Stupnikov, A., et al.
Publicado: (2021)

In Silico Drug Repurposing in Multiple Sclerosis Using scRNA-Seq Data
por: Shevtsov, Andrey, et al.
Publicado: (2023)

Subsampling
por: Politis, Dimitris N, et al.
Publicado: (1999)

Subsampling scaling
por: Levina, A., et al.
Publicado: (2017)

Approaches for sRNA Analysis of Human RNA-Seq Data: Comparison, Benchmarking
por: Bezuglov, Vitalik, et al.
Publicado: (2023)

subSeq: Determining Appropriate Sequencing Depth Through Efficient Read Subsampling
por: Robinson, David G., et al.
Publicado: (2014)

Severe testing with high-dimensional omics data for enhancing biomedical scientific discovery
por: Emmert-Streib, Frank
Publicado: (2022)

A BRCA1 deficient, NFκB driven immune signal predicts good outcome in triple negative breast cancer
por: Buckley, Niamh E., et al.
Publicado: (2016)

Functional and genetic analysis of the colon cancer network
por: Emmert-Streib, Frank, et al.
Publicado: (2014)

Genomic prediction using subsampling
por: Xavier, Alencar, et al.
Publicado: (2017)

Subsampling of cues in associative learning
por: Perez, Omar D., et al.
Publicado: (2022)

The Process of Analyzing Data is the Emergent Feature of Data Science
por: Emmert-Streib, Frank, et al.
Publicado: (2016)

Enhancing systems medicine beyond genotype data by dynamic patient signatures: having information and using it too
por: Emmert-Streib, Frank, et al.
Publicado: (2013)

Data-Driven Computational Social Network Science: Predictive and Inferential Models for Web-Enabled Scientific Discoveries
por: Emmert-Streib, Frank, et al.
Publicado: (2021)

Characterization of Pyroptosis-Related Subtypes via RNA-Seq and ScRNA-Seq to Predict Chemo-Immunotherapy Response in Triple-Negative Breast Cancer
por: Li, Chenlu, et al.
Publicado: (2022)

Characteristics of triple-negative breast cancer
por: de Ruijter, Tim C., et al.
Publicado: (2010)

Systemically Identifying Triple-Negative Breast Cancer Subtype-Specific Prognosis Signatures, Based on Single-Cell RNA-Seq Data
por: Xing, Kaiyuan, et al.
Publicado: (2023)

Quantifying the distance to criticality under subsampling
por: Wilting, Jens, et al.
Publicado: (2015)

Against Dataism and for Data Sharing of Big Biomedical and Clinical Data with Research Parasites
por: Emmert-Streib, Frank, et al.
Publicado: (2016)

Erratum to: Genomic prediction using subsampling
por: Xavier, Alencar, et al.
Publicado: (2017)

What Is a Digital Twin? Experimental Design for a Data-Centric Machine Learning Perspective in Health
por: Emmert-Streib, Frank, et al.
Publicado: (2022)

Single-Cell RNA-Seq Reveals Heterogeneous lncRNA Expression in Xenografted Triple-Negative Breast Cancer Cells
por: Pinkney, Holly R., et al.
Publicado: (2021)

Bagging Statistical Network Inference from Large-Scale Gene Expression Data
por: de Matos Simoes, Ricardo, et al.
Publicado: (2012)

Detecting sequence dependent transcriptional pauses from RNA and protein number time series
por: Emmert-Streib, Frank, et al.
Publicado: (2012)

Data Analytics Applications for Streaming Data From Social Media: What to Predict?
por: Emmert-Streib, Frank, et al.
Publicado: (2018)

Influence of Statistical Estimators of Mutual Information and Data Heterogeneity on the Inference of Gene Regulatory Networks
por: de Matos Simoes, Ricardo, et al.
Publicado: (2011)

A comprehensive survey of error measures for evaluating binary decision making in data science
por: Emmert‐Streib, Frank, et al.
Publicado: (2019)

Limitations of Gene Duplication Models: Evolution of Modules in Protein Interaction Networks
por: Emmert-Streib, Frank
Publicado: (2012)

Cannot write session to /tmp/vufind_sessions/sess_h2ljj8k5tr2hlv1dpstr7g0j8i