Dataset Information

Advanced heat map and clustering analysis using heatmap3.

ABSTRACT: Heat maps and clustering are used frequently in expression analysis studies for data visualization and quality control. Simple clustering and heat maps can be produced from the "heatmap" function in R. However, the "heatmap" function lacks certain functionalities and customizability, preventing it from generating advanced heat maps and dendrograms. To tackle the limitations of the "heatmap" function, we have developed an R package "heatmap3" which significantly improves the original "heatmap" function by adding several more powerful and convenient features. The "heatmap3" package allows users to produce highly customizable state of the art heat maps and dendrograms. The "heatmap3" package is developed based on the "heatmap" function in R, and it is completely compatible with it. The new features of "heatmap3" include highly customizable legends and side annotation, a wider range of color selections, new labeling features which allow users to define multiple layers of phenotype variables, and automatically conducted association tests based on the phenotypes provided. Additional features such as different agglomeration methods for estimating distance between two samples are also added for clustering.

SUBMITTER: Zhao S

PROVIDER: S-EPMC4124803 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Publications

Advanced heat map and clustering analysis using heatmap3.

Zhao Shilin S Zhao Shilin S Guo Yan Y Sheng Quanhu Q Shyr Yu Y

BioMed research international 20140716

Heat maps and clustering are used frequently in expression analysis studies for data visualization and quality control. Simple clustering and heat maps can be produced from the "heatmap" function in R. However, the "heatmap" function lacks certain functionalities and customizability, preventing it from generating advanced heat maps and dendrograms. To tackle the limitations of the "heatmap" function, we have developed an R package "heatmap3" which significantly improves the original "heatmap" fu ...[more]

PMID: 25143956

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Project description:BackgroundMatrix metalloproteinases (MMPs) are well-known biological targets implicated in tumour progression, homeostatic regulation, innate immunity, impaired delivery of pro-apoptotic ligands, and the release and cleavage of cell-surface receptors. With this in mind, the perception of the intimate relationships among diverse MMPs could be a solid basis for accelerated learning in designing new selective MMP inhibitors. In this regard, decrypting the latent molecular reasons in order to elucidate similarity among MMPs is a key challenge.ResultsWe describe a pairwise variant of the non-parametric chaotic map clustering (CMC) algorithm and its application to 104 X-ray MMP structures. In this analysis electrostatic potentials are computed and used as input for the CMC algorithm. It was shown that differences between proteins reflect genuine variation of their electrostatic potentials. In addition, the analysis has been also extended to analyze the protein primary structures and the molecular shapes of the MMP co-crystallised ligands.ConclusionsThe CMC algorithm was shown to be a valuable tool in knowledge acquisition and transfer from MMP structures. Based on the variation of electrostatic potentials, CMC was successful in analysing the MMP target family landscape and different subsites. The first investigation resulted in rational figure interpretation of both domain organization as well as of substrate specificity classifications. The second made it possible to distinguish the MMP classes, demonstrating the high specificity of the S1' pocket, to detect both the occurrence of punctual mutations of ionisable residues and different side-chain conformations that likely account for induced-fit phenomena. In addition, CMC demonstrated a potential comparable to the most popular UPGMA (Unweighted Pair Group Method with Arithmetic mean) method that, at present, represents a standard clustering bioinformatics approach. Interestingly, CMC and UPGMA resulted in closely comparable outcomes, but often CMC produced more informative and more easy interpretable dendrograms. Finally, CMC was successful for standard pairwise analysis (i.e., Smith-Waterman algorithm) of protein sequences and was used to convincingly explain the complementarity existing between the molecular shapes of the co-crystallised ligand molecules and the accessible MMP void volumes.

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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Advanced heat map and clustering analysis using heatmap3.

Publications

Advanced heat map and clustering analysis using heatmap3.

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