Dataset Information

CLEAN: CLustering Enrichment ANalysis.

ABSTRACT: Integration of biological knowledge encoded in various lists of functionally related genes has become one of the most important aspects of analyzing genome-wide functional genomics data. In the context of cluster analysis, functional coherence of clusters established through such analyses have been used to identify biologically meaningful clusters, compare clustering algorithms and identify biological pathways associated with the biological process under investigation.We developed a computational framework for analytically and visually integrating knowledge-based functional categories with the cluster analysis of genomics data. The framework is based on the simple, conceptually appealing, and biologically interpretable gene-specific functional coherence score (CLEAN score). The score is derived by correlating the clustering structure as a whole with functional categories of interest. We directly demonstrate that integrating biological knowledge in this way improves the reproducibility of conclusions derived from cluster analysis. The CLEAN score differentiates between the levels of functional coherence for genes within the same cluster based on their membership in enriched functional categories. We show that this aspect results in higher reproducibility across independent datasets and produces more informative genes for distinguishing different sample types than the scores based on the traditional cluster-wide analysis. We also demonstrate the utility of the CLEAN framework in comparing clusterings produced by different algorithms. CLEAN was implemented as an add-on R package and can be downloaded at http://Clusteranalysis.org. The package integrates routines for calculating gene specific functional coherence scores and the open source interactive Java-based viewer Functional TreeView (FTreeView).Our results indicate that using the gene-specific functional coherence score improves the reproducibility of the conclusions made about clusters of co-expressed genes over using the traditional cluster-wide scores. Using gene-specific coherence scores also simplifies the comparisons of clusterings produced by different clustering algorithms and provides a simple tool for selecting genes with a "functionally coherent" expression profile.

SUBMITTER: Freudenberg JM

PROVIDER: S-EPMC2734555 | biostudies-literature | 2009 Jul

REPOSITORIES: biostudies-literature

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CLEAN: CLustering Enrichment ANalysis.

Freudenberg Johannes M JM Joshi Vineet K VK Hu Zhen Z Medvedovic Mario M

BMC bioinformatics 20090729

<h4>Background</h4>Integration of biological knowledge encoded in various lists of functionally related genes has become one of the most important aspects of analyzing genome-wide functional genomics data. In the context of cluster analysis, functional coherence of clusters established through such analyses have been used to identify biologically meaningful clusters, compare clustering algorithms and identify biological pathways associated with the biological process under investigation.<h4>Resu ...[more]

PMID: 19640299

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Project description:This article contains data related to the research article 'Application of bi-clustering of gene expression data and gene set enrichment analysis methods to identify potentially disease causing nanomaterials' (Williams and Halappanavar, 2015) [1]. The presence of diverse types of nanomaterials (NMs) in commerce has grown significantly in the past decade and as a result, human exposure to these materials in the environment is inevitable. The traditional toxicity testing approaches that are reliant on animals are both time- and cost- intensive; employing which, it is not possible to complete the challenging task of safety assessment of NMs currently on the market in a timely manner. Thus, there is an urgent need for comprehensive understanding of the biological behavior of NMs, and efficient toxicity screening tools that will enable the development of predictive toxicology paradigms suited to rapidly assessing the human health impacts of exposure to NMs. In an effort to predict the long term health impacts of acute exposure to NMs, in Williams and Halappanavar (2015) [1], we applied bi-clustering and gene set enrichment analysis methods to derive essential features of altered lung transcriptome following exposure to NMs that are associated with lung-specific diseases. Several datasets from public microarray repositories describing pulmonary diseases in mouse models following exposure to a variety of substances were examined and functionally related bi-clusters showing similar gene expression profiles were identified. The identified bi-clusters were then used to conduct a gene set enrichment analysis on lung gene expression profiles derived from mice exposed to nano-titanium dioxide, carbon black or carbon nanotubes (nano-TiO2, CB and CNTs) to determine the disease significance of these data-driven gene sets. The results of the analysis correctly identified all NMs to be inflammogenic, and only CB and CNTs as potentially fibrogenic. Here, we elaborate on the details of the statistical methods and algorithms used to derive the disease relevant gene signatures. These details will enable other investigators to use the gene signature in future Gene Set Enrichment Analysis studies involving NMs or as features for clustering and classifying NMs of diverse properties.

Project description:BackgroundThere are 3 issues in bibliometrics that need to be addressed: The lack of a clear definition for author collaborations in cluster analysis that takes into account collaborations with and without self-connections; The need to develop a simple yet effective clustering algorithm for use in coword analysis, and; The inadequacy of general bibliometrics in regard to comparing research achievements and identifying articles that are worth reading and recommended for readers. The study aimed to put forth a clustering algorithm for cluster analysis (called following leader clustering [FLCA], a follower-leading clustering algorithm), examine the dissimilarities in cluster outcomes when considering collaborations with and without self-connections in cluster analysis, and demonstrate the application of the clustering algorithm in bibliometrics.MethodsThe study involved a search for articles and review articles published in JMIR Medical Informatics between 2016 and 2022, conducted using the Web of Science core collections. To identify author collaborations (ACs) and themes over the past 7 years, the study utilized the FLCA algorithm. With the 3 objectives of; Comparing the results obtained from scenarios with and without self-connections; Applying the FLCA algorithm in ACs and themes, and; Reporting the findings using traditional bibliometric approaches based on counts and citations, and all plots were created using R.ResultsThe study found a significant difference in cluster outcomes between the 2 scenarios with and without self-connections, with a 53.8% overlap (14 out of the top 20 countries in ACs). The top clusters were led by Yonsei University in South Korea, Grang Luo from the US, and model in institutes, authors, and themes over the past 7 years. The top entities with the most publications in JMIR Medical Informatics were the United States, Yonsei University in South Korea, Medical School, and Grang Luo from the US.ConclusionThe FLCA algorithm proposed in this study offers researchers a comprehensive approach to exploring and comprehending the complex connections among authors or keywords. The study suggests that future research on ACs with cluster analysis should employ FLCA and R visualizations.

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CLEAN: CLustering Enrichment ANalysis.

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CLEAN: CLustering Enrichment ANalysis.

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