Co-clustering and visualization of gene expression data and gene ontology terms for Saccharomyces cerevisiae using self-organizing maps

No abstract is available for this paper.

• Publication year

  2007

• Venue

  Journal of Biomedical Informatics

• Publication date

  2007-04-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1016/J.JBI.2006.05.001PMID 16824804
• 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.

• Self-Organizing Maps

  2011cited by this paper
• A memetic co-clustering algorithm for gene expression profiles and biological annotation

  2004cited by this paper
• Gene expression correlation and gene ontology-based similarity: an assessment of quantitative relationships

  2004cited by this paper
• A Knowledge-Based Clustering Algorithm Driven by Gene Ontology

  2004cited by this paper
• NetAffx Gene Ontology Mining Tool: a visual approach for microarray data analysis.

  2004cited by this paper
• Evaluation and optimization of clustering in gene expression data analysis

  2004cited by this paper
• Saccharomyces genome database: Underlying principles and organisation

  2004cited by this paper
• Computational Analysis of Microarray Data

  2003cited by this paper
• Predicting gene ontology biological process from temporal gene expression patterns.

  2003cited by this paper
• MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data

  2003cited by this paper
• Investigating Semantic Similarity Measures Across the Gene Ontology: The Relationship Between Sequence and Annotation

  2003cited by this paper
• Co-clustering of biological networks and gene expression data

  2002cited by this paper
• A cluster validity framework for genome expression data

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

  2002cited by this paper
• Judging the quality of gene expression-based clustering methods using gene annotation.

  2002cited by this paper
• Computational genetics: Computational analysis of microarray data

  2001cited by this paper
• Modeling Medical Prognosis: Survival Analysis Techniques

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

  2001cited by this paper
• Knowledge-based analysis of microarray gene expression data by using support vector machines.

  2000cited by this paper
• Gene Ontology: tool for the unification of biology

  2000cited by this paper
• Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation.

  1999cited by this paper
• Molecular classification of cancer: class discovery and class prediction by gene expression monitoring.

  1999cited by this paper
• An Information-Theoretic Definition of Similarity

  1998cited by this paper
• A genome-wide transcriptional analysis of the mitotic cell cycle.

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

  1998cited by this paper
• Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.

  1998cited by this paper
• Semantic Similarity Based on Corpus Statistics and Lexical Taxonomy

  1997cited by this paper
• Using Information Content to Evaluate Semantic Similarity in a Taxonomy

  1995cited by this paper
• A Cluster Separation Measure

  1979cited by this paper
• Well-Separated Clusters and Optimal Fuzzy Partitions

  1974cited by this paper

• Global-local Dirichlet processes for identifying pan-cancer subpopulations using both shared and cancer-specific data

  2025cites this paper
• A sparse exponential family latent block model for co-clustering

  2024cites this paper
• Robust weighted co-clustering with global and local discrimination

  2023cites this paper
• Joint nonnegative matrix factorization and network embedding for graph co-clustering

  2021cites this paper
• DPEBic: detecting essential proteins in gene expressions using encoding and biclustering algorithm

  2021cites this paper
• Application of Artificial Intelligence in Cardiovascular Medicine.

  2021cites this paper
• A Hybrid Algorithm Based Robust Big Data Clustering for Solving Unhealthy Initialization, Dynamic Centroid Selection and Empty clustering Problems with Analysis

  2020cites this paper
• Mining Similar Aspects for Gene Similarity Explanation Based on Gene Information Network

  2020cites this paper
• Gene Function Similarity Method Based on Data Fusion

  2020cites this paper
• A Novel Graph Topology-Based GO-Similarity Measure for Signature Detection From Multi-Omics Data and its Application to Other Problems

  2020cites this paper
• POPBic: Pathway-Based Order Preserving Biclustering Algorithm Towards the Analysis of Gene Expression Data

  2020cites this paper
• A Fuzzy Based Techniques For Energy Efficient Cluster Head Selection For Wireless Sensor Network

  2019cites this paper
• Semantic Similarity in Cheminformatics

  2019cites this paper
• GOGO: An improved algorithm to measure the semantic similarity between gene ontology terms

  2018cites this paper
• Gene Ontology Semi-supervised Clustering for Prediction of Genes Functions

  2018cites this paper
• Incorporating gene ontology into fuzzy relational clustering of microarray gene expression data

  2018cites this paper
• Combining K-Means and a genetic algorithm through a novel arrangement of genetic operators for high quality clustering

  2018cites this paper
• Pairwise gene GO-based measures for biclustering of high-dimensional expression data

  2018cites this paper
• An unsupervised machine learning model for discovering latent infectious diseases using social media data

  2017cites this paper
• Penalized nonnegative matrix tri-factorization for co-clustering

  2017cites this paper
• Robust co-clustering via dual local learning and high-order matrix factorization

  2017cites this paper
• Genetic Algorithm based Clustering Techniques and Tree based Validation in Producing and Evaluating Sensible Clusters

  2017cites this paper
• SGFSC: speeding the gene functional similarity calculation based on hash tables

  2016cites this paper
• An improved computational framework using one stage filtration by incorporating knowledge in gene expression clustering

  2016cites this paper
• Generalized topographic block model

  2016cites this paper
• A Method for the Annotation of Functional Similarities of Coding DNA Sequences: the Case of a Populated Cluster of Transmembrane Proteins

  2016cites this paper
• An improved method for functional similarity analysis of genes based on Gene Ontology

  2016cites this paper
• Inferring Unknown Biological Function by Integration of GO Annotations and Gene Expression Data

  2016cites this paper
• A new path based hybrid measure for gene ontology similarity

  2014cites this paper
• Automatic Selection of High Quality Initial Seeds for Generating High Quality Clusters without requiring any User Inputs

  2014cites this paper
• Leveraging additional knowledge to support coherent bicluster discovery in gene expression data

  2014cites this paper
• A New Path Based Hybrid Measure for Gene Ontology Similarity

  2014cites this paper
• Quantitative Arbor Analytics: Unsupervised Harmonic Co-Clustering of Populations of Brain Cell Arbors Based on L-Measure

  2014cites this paper
• Gene Function Prediction Using Improved Fuzzy c-Means Algorithm

  2014cites this paper
• Measuring gene functional similarity based on group-wise comparison of GO terms

  2013cites this paper
• Multi-stage filtering for improving confidence level and determining dominant clusters in clustering algorithms of gene expression data

  2013cites this paper
• Semi‐supervised clustering methods

  2013cites this paper
• Multi-stage filtering for improving confidence level and determining cp

  2013cites this paper
• Determining the Semantic Similarities Among Gene Ontology Terms

  2013cites this paper
• Coclustering Under Gene Ontology Derived Constraints for Pathway Identification

  2013cites this paper
• Analysis of Tandem Repeat Patterns in Nlrc4 using a Motif Model

  2012cites this paper
• Ontology-based Gene Set Enrichment Analysis Using an Efficient Semantic Similarity Measure and Functional Clustering

  2012cites this paper
• GOcSim: GO context-driven similarity

  2012cites this paper
• Computational Methods for Knowledge Integration in the Analysis of Large-scale Biological Networks

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

  2012cites this paper
• GO-based Functional Dissimilarity of Gene Sets

  2011cites this paper
• Investigating “Gene Ontology”- based semantic similarity in the context of functional genomics

  2011cites this paper
• Benchmarking a new semantic similarity measure using fuzzy clustering and reference sets: Application to cancer expression data

  2011cites this paper
• Ontology-based functional classification of genes: Evaluation with reference sets and overlap analysis

  2011cites this paper
• Prise en compte des connaissances du domaine dans l'analyse transcriptomique : Similarité sémantique, classification fonctionnelle et profils flous. Application au cancer colorectal. (Using domain knowledge in the transcriptome analysis: semantic similarity, functional classification and fuzzy profi

  2011cites this paper
• Efficiently Finding Similar Objects on Ontologies Using Earth Mover's Distance

  2010cites this paper
• Finding Top-k Similar Pairs of Objects Annotated with Terms from an Ontology

  2010influential citation
• A Novel Weighted Functional Similarity Algorithm Applied to Analyze the Protein-protein Interaction*: A Novel Weighted Functional Similarity Algorithm Applied to Analyze the Protein-protein Interaction*

  2010cites this paper
• Learning Distance Functions For Gene Expression Data

  2010influential citation
• Computing With Words With the Ontological

  2010cites this paper
• Computing With Words With the Ontological Self-Organizing Map

  2010cites this paper
• Infectious Disease Ontology

  2010cites this paper
• IntelliGO: a new vector-based semantic similarity measure including annotation origin

  2010cites this paper
• Ontology-Driven Co-clustering of Gene Expression Data

  2009cites this paper
• Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns.

  2009cites this paper
• Fuzzy c-means clustering with prior biological knowledge

  2009cites this paper
• FunSimMat update: new features for exploring functional similarity

  2009cites this paper
• Biomedical Ontologies in Action: Role in Knowledge Management, Data Integration and Decision Support

  2008cites this paper
• Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data

  2008cites this paper
• Short time series microarray data analysis and biological annotation

  2008cites this paper
• Ontological self-organizing maps for cluster visualization and functional summarization of gene products using Gene Ontology similarity measures

  2008cites this paper
• Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies†

  2008cites this paper
• FunSimMat: a comprehensive functional similarity database

  2007cites this paper
• Special Issue: Bio*Medical Informatics

  2007cites this paper
• Fuzzy C-means Clustering with Prior Biological Knowledge

  year unknowncites this paper