Cargando…

Pathway network inference from gene expression data

BACKGROUND: The development of high-throughput omics technologies enabled genome-wide measurements of the activity of cellular elements and provides the analytical resources for the progress of the Systems Biology discipline. Analysis and interpretation of gene expression data has evolved from the g...

Descripción completa

Detalles Bibliográficos
Autores principales:	Ponzoni, Ignacio, Nueda, María José, Tarazona, Sonia, Götz, Stefan, Montaner, David, Dussaut, Julieta Sol, Dopazo, Joaquín, Conesa, Ana
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2014
Materias:	Research
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4101702/ https://www.ncbi.nlm.nih.gov/pubmed/25032889 http://dx.doi.org/10.1186/1752-0509-8-S2-S7

Ejemplares similares

Serial Expression Analysis: a web tool for the analysis of serial gene expression data
por: Nueda, Maria José, et al.
Publicado: (2010)

Functional assessment of time course microarray data
por: Nueda, María José, et al.
Publicado: (2009)

Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series
por: Nueda, María José, et al.
Publicado: (2014)

High-throughput functional annotation and data mining with the Blast2GO suite
por: Götz, Stefan, et al.
Publicado: (2008)

Identification and visualization of differential isoform expression in RNA-seq time series
por: Nueda, María José, et al.
Publicado: (2018)

Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package
por: Tarazona, Sonia, et al.
Publicado: (2015)

Understanding disease mechanisms with models of signaling pathway activities
por: Sebastian-Leon, Patricia, et al.
Publicado: (2014)

SNOW, a web-based tool for the statistical analysis of protein–protein interaction networks
por: Minguez, Pablo, et al.
Publicado: (2009)

Inferring the functional effect of gene expression changes in signaling pathways
por: Sebastián-León, Patricia, et al.
Publicado: (2013)

MultiBaC: an R package to remove batch effects in multi-omic experiments
por: Ugidos, Manuel, et al.
Publicado: (2022)

Inferring the regulatory network behind a gene expression experiment
por: Bleda, Marta, et al.
Publicado: (2012)

Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments
por: Al-Shahrour, Fátima, et al.
Publicado: (2008)

Multidimensional Gene Set Analysis of Genomic Data
por: Montaner, David, et al.
Publicado: (2010)

Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling
por: Medina, Ignacio, et al.
Publicado: (2010)

GEPAS, a web-based tool for microarray data analysis and interpretation
por: Tárraga, Joaquín, et al.
Publicado: (2008)

An Approach to Inferring Transcriptional Regulation Among Genes From Large-Scale Expression Data
por: Herrero, Javier, et al.
Publicado: (2003)

acorde unravels functionally interpretable networks of isoform co-usage from single cell data
por: Arzalluz-Luque, Angeles, et al.
Publicado: (2022)

FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments
por: Al-Shahrour, Fátima, et al.
Publicado: (2007)

Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies
por: Medina, Ignacio, et al.
Publicado: (2009)

Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data
por: García-Alcalde, Fernando, et al.
Publicado: (2011)

Initial Genomics of the Human Nucleolus
por: Németh, Attila, et al.
Publicado: (2010)

RGmatch: matching genomic regions to proximal genes in omics data integration
por: Furió-Tarí, Pedro, et al.
Publicado: (2016)

ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling
por: Conde, Lucía, et al.
Publicado: (2007)

B2G-FAR, a species-centered GO annotation repository
por: Götz, Stefan, et al.
Publicado: (2011)

Four new loci associations discovered by pathway-based and network analyses of the genome-wide variability profile of Hirschsprung’s disease
por: Fernández, Raquel Ma, et al.
Publicado: (2012)

Integrating pathway knowledge with deep neural networks to reduce the dimensionality in single-cell RNA-seq data
por: Gundogdu, Pelin, et al.
Publicado: (2022)

Integrated gene set analysis for microRNA studies
por: Garcia-Garcia, Francisco, et al.
Publicado: (2016)

PaintOmics 3: a web resource for the pathway analysis and visualization of multi-omics data
por: Hernández-de-Diego, Rafael, et al.
Publicado: (2018)

Defining the Genomic Signature of Totipotency and Pluripotency during Early Human Development
por: Galan, Amparo, et al.
Publicado: (2013)

Functional profiling and gene expression analysis of chromosomal copy number alterations
por: Conde, Lucía, et al.
Publicado: (2007)

HPG pore: an efficient and scalable framework for nanopore sequencing data
por: Tarraga, Joaquin, et al.
Publicado: (2016)

Gene set internal coherence in the context of functional profiling
por: Montaner, David, et al.
Publicado: (2009)

Assessing the Biological Significance of Gene Expression Signatures and Co-Expression Modules by Studying Their Network Properties
por: Minguez, Pablo, et al.
Publicado: (2011)

Assessing the impact of mutations found in next generation sequencing data over human signaling pathways
por: Hernansaiz-Ballesteros, Rosa D., et al.
Publicado: (2015)

Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics
por: Conesa, Ana, et al.
Publicado: (2008)

Extensive Translatome Remodeling during ER Stress Response in Mammalian Cells
por: Ventoso, Iván, et al.
Publicado: (2012)

From genes to functional classes in the study of biological systems
por: Al-Shahrour, Fátima, et al.
Publicado: (2007)

Integrating gene and protein expression data with genome-scale metabolic networks to infer functional pathways
por: Pey, Jon, et al.
Publicado: (2013)

Actionable pathways: interactive discovery of therapeutic targets using signaling pathway models
por: Salavert, Francisco, et al.
Publicado: (2016)

Fortunella margarita Transcriptional Reprogramming Triggered by Xanthomonas citri subsp. citri
por: Khalaf, Abeer A, et al.
Publicado: (2011)

Cannot write session to /tmp/vufind_sessions/sess_c321ebo9dfpjgeed815q8705e7