IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Gene Ontology analysis in multiple gene clusters under multiple hypothesis testing framework
Artificial Intelligence in Medicine
Development of Two-Stage SVM-RFE Gene Selection Strategy for Microarray Expression Data Analysis
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Methodological Review: Towards knowledge-based gene expression data mining
Journal of Biomedical Informatics
SEGS: Search for enriched gene sets in microarray data
Journal of Biomedical Informatics
Creating gene set activity profiles with time-series expression data
International Journal of Bioinformatics Research and Applications
Interpreting Gene Expression Data by Searching for Enriched Gene Sets
AIME '07 Proceedings of the 11th conference on Artificial Intelligence in Medicine
An Algorithm to Assess the Reliability of Hierarchical Clusters in Gene Expression Data
KES '08 Proceedings of the 12th international conference on Knowledge-Based Intelligent Information and Engineering Systems, Part III
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Complex phylogenetic profiling reveals fundamental genotype-phenotype associations
Computational Biology and Chemistry
Formulating and testing hypotheses in functional genomics
Artificial Intelligence in Medicine
Relational Descriptive Analysis of Gene Expression Data
Proceedings of the 2006 conference on STAIRS 2006: Proceedings of the Third Starting AI Researchers' Symposium
Interpretation of gene expression microarray experiments
Proceedings of the 2007 conference on Emerging Artificial Intelligence Applications in Computer Engineering: Real Word AI Systems with Applications in eHealth, HCI, Information Retrieval and Pervasive Technologies
A stability-based algorithm to validate hierarchical clusters of genes
International Journal of Knowledge Engineering and Soft Data Paradigms
SoFoCles: Feature filtering for microarray classification based on Gene Ontology
Journal of Biomedical Informatics
Data-Fusion in Clustering Microarray Data: Balancing Discovery and Interpretability
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Predicting Novel Human Gene Ontology Annotations Using Semantic Analysis
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Discovering relations among GO-annotated clusters by Graph Kernel methods
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
Efficient generation of biologically relevant enriched gene sets
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
Evaluating graph kernel methods for relation discovery in GO-annotated clusters
KES'07/WIRN'07 Proceedings of the 11th international conference, KES 2007 and XVII Italian workshop on neural networks conference on Knowledge-based intelligent information and engineering systems: Part III
A system biology approach for the steady-state analysis of gene signaling networks
CIARP'07 Proceedings of the Congress on pattern recognition 12th Iberoamerican conference on Progress in pattern recognition, image analysis and applications
Construction of gene networks with hybrid approach from expression profile and gene ontology
IEEE Transactions on Information Technology in Biomedicine
Pattern Recognition Letters
Finding microarray genes using GO ontology
Proceedings of the 1st Amrita ACM-W Celebration on Women in Computing in India
Ontology consolidation in bioinformatics
APCCM '10 Proceedings of the Seventh Asia-Pacific Conference on Conceptual Modelling - Volume 110
Independent component analysis: Mining microarray data for fundamental human gene expression modules
Journal of Biomedical Informatics
Dynamic ontology version control
Proceedings of the 48th Annual Southeast Regional Conference
Data integration and knowledge discovery in life sciences
IEA/AIE'10 Proceedings of the 23rd international conference on Industrial engineering and other applications of applied intelligent systems - Volume Part III
Desiderata for ontologies to be used in semantic annotation of biomedical documents
Journal of Biomedical Informatics
A systematic comparison of genome scale clustering algorithms
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
Discovering the transcriptional modules using microarray data by penalized matrix decomposition
Computers in Biology and Medicine
CarGene: Characterisation of sets of genes based on metabolic pathways analysis
International Journal of Data Mining and Bioinformatics
International Journal of Applied Mathematics and Computer Science
Gene ontology based automated annotation: why it isn't working
ER'11 Proceedings of the 30th international conference on Advances in conceptual modeling: recent developments and new directions
Enabling enrichment analysis with the Human Disease Ontology
Journal of Biomedical Informatics
The multi-reference contrast method: Facilitating set enrichment analysis
Computers in Biology and Medicine
iPlant atmosphere: a gateway to cloud infrastructure for the plant sciences
Proceedings of the 2011 ACM workshop on Gateway computing environments
Relational subgroup discovery for descriptive analysis of microarray data
CompLife'06 Proceedings of the Second international conference on Computational Life Sciences
Incorporating biological domain knowledge into cluster validity assessment
EuroGP'06 Proceedings of the 2006 international conference on Applications of Evolutionary Computing
Sensitive detection of pathway perturbations in cancers: extended abstract
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Semi-bipartite graph visualization for gene ontology networks
GD'09 Proceedings of the 17th international conference on Graph Drawing
An improved statistic for detecting over-represented gene ontology annotations in gene sets
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Contrast mining from interesting subgroups
Bisociative Knowledge Discovery
AOW '07 Proceedings of the Third Australasian Workshop on Advances in Ontologies - Volume 85
Journal of Web Engineering
Comparative meta-analysis between human and mouse cancer microarray data reveals critical pathways
International Journal of Data Mining and Bioinformatics
Incorporation of gene exchangeabilities improves the reproducibility of gene set rankings
Computational Statistics & Data Analysis
Functional interpretation of microRNA-mRNA association in biological systems using R
Computers in Biology and Medicine
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Summary: Independent of the platform and the analysis methods used, the result of a microarray experiment is, in most cases, a list of differentially expressed genes. An automatic ontological analysis approach has been recently proposed to help with the biological interpretation of such results. Currently, this approach is the de facto standard for the secondary analysis of high throughput experiments and a large number of tools have been developed for this purpose. We present a detailed comparison of 14 such tools using the following criteria: scope of the analysis, visualization capabilities, statistical model(s) used, correction for multiple comparisons, reference microarrays available, installation issues and sources of annotation data. This detailed analysis of the capabilities of these tools will help researchers choose the most appropriate tool for a given type of analysis. More importantly, in spite of the fact that this type of analysis has been generally adopted, this approach has several important intrinsic drawbacks. These drawbacks are associated with all tools discussed and represent conceptual limitations of the current state-of-the-art in ontological analysis. We propose these as challenges for the next generation of secondary data analysis tools. Contact: sod@cs.wayne.edu