Cargando…

Hunting complex differential gene interaction patterns across molecular contexts

Heterogeneity in genetic networks across different signaling molecular contexts can suggest molecular regulatory mechanisms. Here we describe a comparative chi-square analysis (CPχ(2)) method, considerably more flexible and effective than other alternatives, to screen large gene expression data sets...

Descripción completa

Detalles Bibliográficos
Autores principales:	Song, Mingzhou, Zhang, Yang, Katzaroff, Alexia J., Edgar, Bruce A., Buttitta, Laura
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2014
Materias:	Methods Online
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3985659/ https://www.ncbi.nlm.nih.gov/pubmed/24482443 http://dx.doi.org/10.1093/nar/gku086

Ejemplares similares

A robust cell cycle control mechanism limits E2F-induced proliferation of terminally differentiated cells in vivo
por: Buttitta, Laura A., et al.
Publicado: (2010)

Inferring and modeling inheritance of differentially methylated changes across multiple generations
por: Belleau, Pascal, et al.
Publicado: (2018)

Data-driven characterization of molecular phenotypes across heterogeneous sample collections
por: Mehtonen, Juha, et al.
Publicado: (2019)

Discover context-specific combinatorial transcription factor interactions by integrating diverse ChIP-Seq data sets
por: Teng, Li, et al.
Publicado: (2014)

Locating, tracing and sequencing multiple expanded genetic letters in complex DNA context via a bridge-base approach
por: Wang, Honglei, et al.
Publicado: (2023)

HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins
por: Zhang, Fuhao, et al.
Publicado: (2023)

Joint Bayesian inference of risk variants and tissue-specific epigenomic enrichments across multiple complex human diseases
por: Li, Yue, et al.
Publicado: (2016)

DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts
por: Catoni, Marco, et al.
Publicado: (2018)

Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions
por: Betts, Matthew J., et al.
Publicado: (2015)

A rapid assay for affinity and kinetics of molecular interactions with nucleic acids
por: Donaldson, Gregory P., et al.
Publicado: (2012)

Systematic integration of RNA-Seq statistical algorithms for accurate detection of differential gene expression patterns
por: Moulos, Panagiotis, et al.
Publicado: (2015)

Integrating probe-level expression changes across generations of Affymetrix arrays
por: Elo, Laura L., et al.
Publicado: (2005)

A novel transcriptome subtraction method for the detection of differentially expressed genes in highly complex eukaryotes
por: Li, L., et al.
Publicado: (2005)

Universal correction of enzymatic sequence bias reveals molecular signatures of protein/DNA interactions
por: Martins, André L, et al.
Publicado: (2018)

TFregulomeR reveals transcription factors’ context-specific features and functions
por: Lin, Quy Xiao Xuan, et al.
Publicado: (2020)

Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation
por: Poppleton, Erik, et al.
Publicado: (2020)

COMET: adaptive context-based modeling for ultrafast HIV-1 subtype identification
por: Struck, Daniel, et al.
Publicado: (2014)

ME-Class2 reveals context dependent regulatory roles for 5-hydroxymethylcytosine
por: Schlosberg, Christopher E, et al.
Publicado: (2019)

Modular 5′-UTR hexamers for context-independent tuning of protein expression in eukaryotes
por: Petersen, Søren D, et al.
Publicado: (2018)

Analysis of factor interactions with RNA polymerase II elongation complexes using a new electrophoretic mobility shift assay
por: Cheng, Bo, et al.
Publicado: (2008)

Epi-MEIF: detecting higher order epistatic interactions for complex traits using mixed effect conditional inference forests
por: Saha, Saswati, et al.
Publicado: (2022)

Accurately annotate compound effects of genetic variants using a context-sensitive framework
por: Cheng, Si-Jin, et al.
Publicado: (2017)

Novel bioinformatics quality control metric for next-generation sequencing experiments in the clinical context
por: Ivanov, Maxim, et al.
Publicado: (2019)

Molecule-level imaging of Pax6 mRNA distribution in mouse embryonic neocortex by molecular interaction force microscopy
por: Jung, Yu Jin, et al.
Publicado: (2009)

A designed RNA selection: establishment of a stable complex between a target and selectant RNA via two coordinated interactions
por: Shiohara, Tomoaki, et al.
Publicado: (2009)

A pHMM-ANN based discriminative approach to promoter identification in prokaryote genomic contexts
por: Mann, Scott, et al.
Publicado: (2007)

Gene integrated set profile analysis: a context-based approach for inferring biological endpoints
por: Kowalski, Jeanne, et al.
Publicado: (2016)

Turning publicly available gene expression data into discoveries using gene set context analysis
por: Ji, Zhicheng, et al.
Publicado: (2016)

Coexisting/Coexpressing Genomic Libraries (CoGeL) identify interactions among distantly located genetic loci for developing complex microbial phenotypes
por: Nicolaou, Sergios A., et al.
Publicado: (2011)

ModuleBlast: identifying activated sub-networks within and across species
por: Zinman, Guy E., et al.
Publicado: (2015)

Rank-in: enabling integrative analysis across microarray and RNA-seq for cancer
por: Tang, Kailin, et al.
Publicado: (2021)

NetDecoder: a network biology platform that decodes context-specific biological networks and gene activities
por: da Rocha, Edroaldo Lummertz, et al.
Publicado: (2016)

Accurate characterization of weak macromolecular interactions by titration of NMR residual dipolar couplings: application to the CD2AP SH3-C:ubiquitin complex
por: Ortega-Roldan, Jose Luis, et al.
Publicado: (2009)

Differential expression analysis for RNAseq using Poisson mixed models
por: Sun, Shiquan, et al.
Publicado: (2017)

riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions
por: Waters, Nicholas R, et al.
Publicado: (2018)

Native gel electrophoresis of human telomerase distinguishes active complexes with or without dyskerin
por: Gardano, Laura, et al.
Publicado: (2012)

A structural-alphabet-based strategy for finding structural motifs across protein families
por: Wu, Chih Yuan, et al.
Publicado: (2010)

Analysis of splicing patterns by pyrosequencing
por: Méreau, Agnès, et al.
Publicado: (2009)

A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria
por: Ou, Hong-Yu, et al.
Publicado: (2006)

CrossHub: a tool for multi-way analysis of The Cancer Genome Atlas (TCGA) in the context of gene expression regulation mechanisms
por: Krasnov, George S., et al.
Publicado: (2016)

Cannot write session to /tmp/vufind_sessions/sess_sasnlc0g7mf3igugcjo40lrfor