Consensus clustering and functional interpretation of gene-expression data

Microarray analysis using clustering algorithms can suffer from lack of inter-method consistency in assigning related gene-expression profiles to clusters. Obtaining a consensus set of clusters from a number of clustering methods should improve confidence in gene-expression analysis. Here we introduce consensus clustering, which provides such an advantage. When coupled with a statistically based gene functional analysis, our method allowed the identification of novel genes regulated by NFκB and the unfolded protein response in certain B-cell lymphomas.

• Publication year

  2004

• Venue

  Genome Biology

• Publication date

  2004-11-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1186/gb-2004-5-11-r94PMID 15535870PMCID 545785
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• [''R"--project for statistical computing].

  2008cited by this paper
• Erratum: Identification of NF-κB-regulated genes induced by TNFα utilizing expression profiling and RNA interference (Oncogene (2003) 22 (2054-2064) doi:10.1038/sj.onc.1206262)

  2004cited by this paper
• DAVID: Database for Annotation, Visualization, and Integrated Discovery

  2003cited by this paper
• Consensus Clustering: A Resampling-Based Method for Class Discovery and Visualization of Gene Expression Microarray Data

  2003influential reference
• A time-dependent phase shift in the mammalian unfolded protein response.

  2003influential reference
• Comparisons and validation of statistical clustering techniques for microarray gene expression data

  2003cited by this paper
• Clustering gene-expression data with repeated measurements

  2003influential reference
• NF-κB-Dependent Assembly of an Enhanceosome-Like Complex on the Promoter Region of Apoptosis Inhibitor Bfl-1/A1

  2003cited by this paper
• Bagging to Improve the Accuracy of A Clustering Procedure

  2003cited by this paper
• Identification of NF-κB-regulated genes induced by TNFα utilizing expression profiling and RNA interference

  2003cited by this paper
• Computationally identifying novel NF-kappa B-regulated immune genes in the human genome.

  2003cited by this paper
• Identification of NF-kappa B-regulated genes induced by TNFalpha utilizing expression profiling and RNA interference.

  2003cited by this paper
• DAVID: Database for Annotation, Visualization, and Integrated Discovery

  2003cited by this paper
• Kaposi's sarcoma-associated herpesvirus-infected primary effusion lymphoma has a plasma cell gene expression profile

  2003influential reference
• Computational Analysis of Microarray Data

  2003cited by this paper
• Computationally Identifying Novel NF-κB-Regulated Immune Genes in the Human Genome

  2003cited by this paper
• Methods for assessing reproducibility of clustering patterns observed in analyses of microarray data

  2002cited by this paper
• Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters

  2002influential reference
• Judging the quality of gene expression-based clustering methods using gene annotation.

  2002influential reference
• IRE1 couples endoplasmic reticulum load to secretory capacity by processing the XBP-1 mRNA

  2002influential reference
• IRE1-mediated unconventional mRNA splicing and S2P-mediated ATF6 cleavage merge to regulate XBP1 in signaling the unfolded protein response.

  2002cited by this paper
• The Ensembl genome database project

  2002cited by this paper
• GeneCardsTM 2002: towards a complete, object-oriented, human gene compendium

  2002cited by this paper
• Statistical estimation of cluster boundaries in gene expression profile data

  2001cited by this paper
• XBP1 mRNA is induced by ATF6 and spliced by IRE1 in response to ER stress to produce a highly active transcription factor.

  2001cited by this paper
• Comparing, Contrasting and Combining Clusters in Viral Gene Expression

  2001cited by this paper
• Bootstrapping cluster analysis: Assessing the reliability of conclusions from microarray experiments

  2001cited by this paper
• STATISTICAL ISSUES IN THE CLUSTERING OF GENE EXPRESSION DATA

  2001cited by this paper
• Computational genetics: Computational analysis of microarray data

  2001cited by this paper
• Validating clustering for gene expression data

  2001influential reference
• Analysis of temporal gene expression profiles: clustering by simulated annealing and determining the optimal number of clusters

  2001cited by this paper
• Variable grouping in multivariate time series via correlation

  2001cited by this paper
• Genomic expression programs in the response of yeast cells to environmental changes.

  2000cited by this paper
• The GRID: Blueprint for a New Computing Infrastructure

  2000cited by this paper
• JPred : a consensus secondary structure prediction server

  1999cited by this paper
• Regulation of the dolichol pathway in human fibroblasts by the endoplasmic reticulum unfolded protein response.

  1999cited by this paper
• Clustering Gene Expression Patterns

  1999cited by this paper
• Mammalian transcription factor ATF6 is synthesized as a transmembrane protein and activated by proteolysis in response to endoplasmic reticulum stress.

  1999cited by this paper
• NF-kappa B and Rel proteins: evolutionarily conserved mediators of immune responses.

  1998cited by this paper
• Genetic Algorithms and Grouping Problems

  1998cited by this paper
• The Grid 2: Blueprint for a New Computing Infrastructure

  1998cited by this paper
• Cluster analysis and display of genome-wide expression patterns.

  1998influential reference
• JPred: a consensus secondary structure prediction server

  1998cited by this paper
• Identification of the cis-Acting Endoplasmic Reticulum Stress Response Element Responsible for Transcriptional Induction of Mammalian Glucose-regulated Proteins

  1998cited by this paper
• BCM Search Launcher--an integrated interface to molecular biology data base search and analysis services available on the World Wide Web.

  1996cited by this paper
• Practical statistics for medical research

  1990influential reference
• Self-organization and associative memory: 3rd edition

  1989cited by this paper
• Self-Organization and Associative Memory

  1988cited by this paper
• Clustering by means of medoids

  1987influential reference
• Optimization by Simulated Annealing

  1983cited by this paper
• STATISTICAL METHODS

  1967cited by this paper
• Some methods for classification and analysis of multivariate observations

  1967cited by this paper
• Hierarchical Grouping to Optimize an Objective Function

  1963influential reference

• ENO1-related gene signature predicts prognosis and therapeutic response in diffuse large B-cell lymphoma

  2025cites this paper
• Integrin-linked kinase control dental pulp stem cell senescence via the mTOR signaling pathway

  2024cites this paper
• Large-Scale Comparative Analysis of Canine and Human Osteosarcomas Uncovers Conserved Clinically Relevant Tumor Microenvironment Subtypes

  2024cites this paper
• A novel comprehensive investigation for enhancing cluster analysis accuracy through ensemble learning methods

  2024cites this paper
• Unveiling the intricate interplay: Exploring biological bridges between renal ischemia-reperfusion injury and T cell-mediated immune rejection in kidney transplantation

  2024cites this paper
• Distinct brain morphometry patterns revealed by deep learning improve prediction of post-stroke aphasia severity

  2024cites this paper
• Distinct brain morphometry patterns revealed by deep learning improve prediction of aphasia severity

  2023cites this paper
• Genes associated with cellular senescence favor melanoma prognosis by stimulating immune responses in tumor microenvironment

  2023cites this paper
• A Broad m6A Modification Landscape in Inflammatory Bowel Disease

  2022cites this paper
• Construction of m7G subtype classification on heterogeneity of sepsis

  2022cites this paper
• Stronger Together: On Combining Relationships in Architectural Recovery Approaches

  2022cites this paper
• Identifying Potential Tumor Antigens and Antigens-Related Subtypes in Hepatocellular Carcinoma for mRNA Vaccine Development

  2022cites this paper
• Estimating the Optimal Number of Clusters from Subsets of Ensembles

  2022influential citation
• An integrated bioinformatic investigation of mitochondrial solute carrier family 25 (SLC25) in colon cancer followed by preliminary validation of member 5 (SLC25A5) in tumorigenesis

  2022cites this paper
• m6A RNA Methylation Regulators Elicit Malignant Progression and Predict Clinical Outcome in Hepatocellular Carcinoma

  2021cites this paper
• Unsupervised Algorithms for Microarray Sample Stratification.

  2021cites this paper
• Identification of gastric cancer subtypes based on pathway clustering

  2021cites this paper
• COMTOP: Protein Residue–Residue Contact Prediction through Mixed Integer Linear Optimization

  2021cites this paper
• A consensus multi-view multi-objective gene selection approach for improved sample classification

  2020cites this paper
• Expression pattern of m6A regulators is significantly correlated with malignancy and antitumor immune response of breast cancer

  2020cites this paper
• Opening the black box: Personalizing type 2 diabetes patients based on their latent phenotype and temporal associated complication rules

  2020cites this paper
• Cluster Ensembles

  2019cites this paper
• Fine-tuned adaptation of embryo–endometrium pairs at implantation revealed by transcriptome analyses in Bos taurus

  2019cites this paper
• Consensus Function Based on Clusters Clustering and Iterative Fusion of Base Clusters

  2019cites this paper
• Opening the Black Box: Exploring Temporal Pattern of Type 2 Diabetes Complications in Patient Clustering Using Association Rules and Hidden Variable Discovery

  2019cites this paper
• Tumour-specific Causal Inference Discovers Distinct Disease Mechanisms Underlying Cancer Subtypes

  2019cites this paper
• Combining clustering and classification ensembles: A novel pipeline to identify breast cancer profiles

  2019cites this paper
• An application of generalised simulated annealing towards the simultaneous modelling and clustering of glaucoma

  2019cites this paper
• Clustering ensemble method

  2018cites this paper
• Integrated genomic analysis identifies clinically relevant subtypes of renal clear cell carcinoma

  2018cites this paper
• β-Catenin–mediated immune evasion pathway frequently operates in primary cutaneous melanomas

  2018cites this paper
• An Effective Data Analysis on Spectral Clustering & Semi Supervised Consensus Spectral Clustering using Consistent Iris Datasets.

  2018cites this paper
• Fine-tuned adaptation of embryo-endometrium pairs at implantation revealed by gene regulatory networks Tailored conceptus-maternal communication at implantation

  2018cites this paper
• Nearest Consensus Clustering Classification to Identify Subclasses and Predict Disease

  2018cites this paper
• Transactions on Large-Scale Data- and Knowledge-Centered Systems IX

  2018cites this paper
• Cluster ensembles: A survey of approaches with recent extensions and applications

  2018cites this paper
• Partitioning of functional gene expression data using principal points

  2017cites this paper
• A stability analysis of sparse K-means

  2017cites this paper
• Integrative Sparse K-Means With Overlapping Group Lasso in Genomic Applications for Disease Subtype Discovery.

  2017cites this paper
• Cluster ensemble based on Random Forests for genetic data

  2017cites this paper
• 2009) ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization. BMC Bioinformatics

  2017cites this paper
• Statistical integrative omics methods for disease subtype discovery

  2017cites this paper
• Stability analysis of MTopGO for module identification in PPI networks

  2017cites this paper
• Systematic Reconstruction of Molecular Cascades Regulating GP Development Using Single-Cell RNA-Seq.

  2016cites this paper
• Simultaneous Modelling and Clustering of Visual Field Data

  2016influential citation
• A Survey of Computational Methods for Protein Function Prediction

  2016influential citation
• Meta-Analytic Framework for Sparse K-Means to Identify Disease Subtypes in Multiple Transcriptomic Studies

  2016cites this paper
• Big Data Analytics in Genomics

  2016cites this paper
• Validation of a Quantifier-Based Fuzzy Classification System for Breast Cancer Patients on External Independent Cohorts

  2016cites this paper
• Structured feature selection using coordinate descent optimization

  2016cites this paper
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  2016cites this paper
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  2016cites this paper
• An integrated clustering analysis framework for heterogeneous data

  2016cites this paper
• Gene masking - a technique to improve accuracy for cancer classification with high dimensionality in microarray data

  2016cites this paper
• Pattern recognition methods to relate time profiles of gene expression with phenotypic data: a comparative study

  2015cites this paper
• A new consensus function based on dual-similarity measurements for clustering ensemble

  2015cites this paper
• Integrating Gene Regulatory Networks to identify cancer-specific genes

  2015cites this paper
• The Information Filtering of Gene Network for Chronic Diseases: Social Network Perspective

  2015cites this paper
• Clustering Methods Discussion

  2015cites this paper
• Collective analysis of multiple high-throughput gene expression datasets

  2015cites this paper
• Interpolation based consensus clustering for gene expression time series

  2015cites this paper
• Consensus methods for virtual screening and clustering of chemical structure databases

  2015cites this paper
• Critical limitations of consensus clustering in class discovery

  2014cites this paper
• Discovering Study-Specific Gene Regulatory Networks

  2014cites this paper
• Semi-supervised consensus clustering for gene expression data analysis

  2014cites this paper
• Handbook of Cluster Analysis (provisional top level file)

  2014cites this paper
• Consensus clustering for urban land use analysis using cell phone network data

  2014influential citation
• Extracting Predictive Models from Marked-Up Free-Text Documents at the Royal Botanic Gardens, Kew, London

  2014cites this paper
• Least Square Consensus Clustering: Criteria, Methods, Experiments

  2013cites this paper
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  2013cites this paper
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  2013cites this paper
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  2013cites this paper
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  2013cites this paper
• Individual Approximate Clusters: Methods, Properties, Applications

  2013cites this paper
• Pairwise Similarity for Cluster Ensemble Problem: Link-Based and Approximate Approaches

  2013cites this paper
• Summary and Semi-average Similarity Criteria for Individual Clusters

  2013cites this paper
• CONCORD: a consensus method for protein secondary structure prediction via mixed integer linear optimization

  2012influential citation
• Data Clustering : Algorithms and Applications

  2012cites this paper
• Combining multiple classifications of chemical structures using consensus clustering.

  2012cites this paper
• Pattern discovery from patient controlled analgesia demand behavior

  2012cites this paper
• Evolution and diversity of periplasmic proteins involved in copper homeostasis in gamma proteobacteria

  2012cites this paper
• Pathway Based Microarray Analysis, Utilising Enzyme Compounds and Cascade Events

  2012influential citation
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  2012cites this paper
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  2012cites this paper
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  2012cites this paper
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  2012cites this paper
• Similitud funcional de genes basada en conocimiento biológico

  2012cites this paper
• Identification of Breast Cancer Subtypes Using Multiple Gene Expression Microarray Datasets

  2011cites this paper
• Robust consensus clustering for identification of expressed genes linked to malignancy of human colorectal carcinoma

  2011cites this paper
• Multi-membership gene regulation in pathway based microarray analysis

  2011cites this paper
• Cluster ensembles

  2011cites this paper
• Munch: An Efficient Modularisation Strategy to Assess the Degree of Refactoring on Sequential Source Code Checkings

  2011cites this paper
• Intelligent Data Analysis for complex systems

  2011cites this paper
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  2011cites this paper
• Peakbin Selection in Mass Spectrometry Data Using a Consensus Approach with Estimation of Distribution Algorithms

  2011cites this paper
• Pathway based microarray analysis based on multi-membership gene regulation

  2011cites this paper
• Similarity clustering of proteins using substantive knowledge and reconstruction of evolutionary gene histories in herpesvirus

  2010cites this paper
• Prédictions contrôlées en apprentissage automatique

  2010cites this paper
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  2010cites this paper
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  2010influential citation