Similarity Analysis by Reciprocal Pairs for Discrete and Continuous Data

McQuitty, Louis L.

doi:10.1177/001316446602600402

Cited by 159 publications

(87 citation statements)

References 2 publications

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“…Next, a symmetric matrix E = (D + D T ) / 2 was created. We then used E to hierarchically cluster the LRR proteins with the method of McQuitty (38) and the hclust function in the R programming language. The clustering result was combined with positional information for each LRR class in each LRR protein using a Perl program and visualized using the representation scheme described previously (39).…”

Section: Methodsmentioning

confidence: 99%

Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity

Eisenberg

Heath

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

181

185

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In innate immune sensing, the detection of pathogen-associated molecular patterns by recognition receptors typically involve leucine-rich repeats (LRRs). We provide a categorization of 375 human LRR-containing proteins, almost half of which lack other identifiable functional domains. We clustered human LRR proteins by first assigning LRRs to LRR classes and then grouping the proteins based on these class assignments, revealing several of the resulting protein groups containing a large number of proteins with certain non-LRR functional domains. In particular, a statistically significantnumber of LRR proteins in the typical (T) and bacterial + typical (S+T) categories have transmembrane domains, whereas most of the LRR proteins in the cysteine-containing (CC) category contain an F-box domain (which mediates interactions with the E3 ubiquitin ligase complex). Furthermore, by examining the evolutionary profiles of the LRR proteins, we identified a subset of LRR proteins exhibiting strong conservation in fungi and an enrichment for "nucleic acid-binding" function. Expression analysis of LRR genes identifies a subset of pathogen-responsive genes in human primary macrophages infected with pathogenic bacteria. Using functional RNAi, we show that MFHAS1 regulates Toll-like receptor (TLR)-dependent signaling. By using protein interaction network analysis followed by functional RNAi, we identified LRSAM1 as a component of the antibacterial autophagic response.pathogen-response | anti-bacterial | inflammation | pathogen sensors | autophagy

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Section: Methodsmentioning

confidence: 99%

Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity

Eisenberg

Heath

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

181

185

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“…Several agglomeration methods are also provided by the NbClust package, namely: Ward (Ward 1963), single (Florek, Lukaszewicz, Perkal, and Zubrzycki 1951;Sokal and Michener 1958), complete (Sørensen 1948), average (Sokal and Michener 1958), McQuitty (McQuitty 1966), median (Gower 1967) and centroid (Sokal and Michener 1958). All of these methods and distance measures are described in detail in Section 3.…”

Section: Indexmentioning

confidence: 99%

NbClust: AnRPackage for Determining the Relevant Number of Clusters in a Data Set

Charrad¹,

Ghazzali²,

Boiteau³

et al. 2014

J. Stat. Soft.

2,405

1,764

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Clustering is the partitioning of a set of objects into groups (clusters) so that objects within a group are more similar to each others than objects in different groups. Most of the clustering algorithms depend on some assumptions in order to define the subgroups present in a data set. As a consequence, the resulting clustering scheme requires some sort of evaluation as regards its validity.The evaluation procedure has to tackle difficult problems such as the quality of clusters, the degree with which a clustering scheme fits a specific data set and the optimal number of clusters in a partitioning. In the literature, a wide variety of indices have been proposed to find the optimal number of clusters in a partitioning of a data set during the clustering process. However, for most of indices proposed in the literature, programs are unavailable to test these indices and compare them.The R package NbClust has been developed for that purpose. It provides 30 indices which determine the number of clusters in a data set and it offers also the best clustering scheme from different results to the user. In addition, it provides a function to perform k-means and hierarchical clustering with different distance measures and aggregation methods. Any combination of validation indices and clustering methods can be requested in a single function call. This enables the user to simultaneously evaluate several clustering schemes while varying the number of clusters, to help determining the most appropriate number of clusters for the data set of interest.

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“…It can be defined, for example as the distance of the elements that are the farthest away in two clusters (complete-linkage;Sorensen 1948), the shortest distance between two elements not yet belonging to the same cluster (single; Sokal & Michener 1958), the average distance of the elements inside two clusters (average; Sokal & Michener 1958), and the squared Euclidean distance between the gravity centres of two clusters (centroid; Sokal & Michener 1958). Linkage criteria also can be determined with the weighted mean of the between-cluster distances (McQuitty;McQuitty 1966), the median of the between-cluster distances (median; Gower 1966), or with minimizing withincluster variance (Ward and its second variant;Ward 1963;Murtagh & Legendre 2014).…”

Section: C3 Hierarchical Clusteringmentioning

confidence: 99%

Structure and stability in TMC-1: Analysis of NH₃molecular line andHerschelcontinuum data

Fehér

Tóth

Ward-Thompson

et al. 2016

A&A

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Aims. We examined the velocity, density, and temperature structure of Taurus molecular cloud-1 (TMC-1), a filamentary cloud in a nearby quiescent star forming area, to understand its morphology and evolution. Methods. We observed high signal-to-noise (S/N), high velocity resolution NH 3 (1,1), and (2, 2) emission on an extended map. By fitting multiple hyperfine-split line profiles to the NH 3 (1, 1) spectra, we derived the velocity distribution of the line components and calculated gas parameters on several positions. Herschel SPIRE far-infrared continuum observations were reduced and used to calculate the physical parameters of the Planck Galactic Cold Clumps (PGCCs) in the region, including the two in TMC-1. The morphology of TMC-1 was investigated with several types of clustering methods in the parameter space consisting of position, velocity, and column density. Results. Our Herschel-based column density map shows a main ridge with two local maxima and a separated peak to the south-west. The H 2 column densities and dust colour temperatures are in the range of 0.5−3.3 × 10 22 cm −2 and 10.5−12 K, respectively. The NH 3 column densities and H 2 volume densities are in the range of 2.8−14.2 × 10 14 cm −2 and 0.4−2.8 × 10 4 cm −3 . Kinetic temperatures are typically very low with a minimum of 9 K at the maximum NH 3 and H 2 column density region. The kinetic temperature maximum was found at the protostar IRAS 04381+2540 with a value of 13.7 K. The kinetic temperatures vary similarly to the colour temperatures in spite of the fact that densities are lower than the critical density for coupling between the gas and dust phase. The k-means clustering method separated four sub-filaments in TMC-1 with masses of 32.5, 19.6, 28.9, and 45.9 M and low turbulent velocity dispersion in the range of 0.13−0.2 km s −1 . Conclusions. The main ridge of TMC-1 is composed of four sub-filaments that are close to gravitational equilibrium. We label these TMC-1F1 through F4. The sub-filaments TMC-1F1, TMC-1F2, and TMC-1F4 are very elongated, dense, and cold. TMC-1F3 is a little less elongated and somewhat warmer, and probably heated by the Class I protostar, IRAS 04381+2540, which is embedded in it. TMC-1F3 is approximately 0.1 pc behind TMC1-F1. Because of its structure, TMC-1 is a good target to test filament evolution scenarios.

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Similarity Analysis by Reciprocal Pairs for Discrete and Continuous Data

Cited by 159 publications

References 2 publications

Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity

Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity

NbClust: AnRPackage for Determining the Relevant Number of Clusters in a Data Set

Structure and stability in TMC-1: Analysis of NH₃molecular line andHerschelcontinuum data

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Similarity Analysis by Reciprocal Pairs for Discrete and Continuous Data

Cited by 159 publications

References 2 publications

Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity

Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity

NbClust: AnRPackage for Determining the Relevant Number of Clusters in a Data Set

Structure and stability in TMC-1: Analysis of NH3molecular line andHerschelcontinuum data

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Structure and stability in TMC-1: Analysis of NH₃molecular line andHerschelcontinuum data