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  • genes
  • We have found in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function, and we find a similar tendency in human data. (pnas.org)
  • It is not the purpose of this paper to survey the various methods available to cluster genes on the basis of their expression patterns, but rather to illustrate how such methods can be useful to biologists in the analysis of gene expression data. (pnas.org)
  • The approach utilizes an analysis of variance model to achieve normalization and estimate differential expression of genes across multiple conditions. (pnas.org)
  • Specifically, an assortment of clustering techniques have been developed and applied to identify groups of genes with similar patterns of expression ( 3 - 6 ). (pnas.org)
  • Consider two genes that cluster together. (pnas.org)
  • Are the patterns of expression for these genes sufficiently similar beyond any reasonable doubts raised by the uncertainty of the estimates, or could these genes have clustered together by chance? (pnas.org)
  • By "clustering" genes, we mean organizing genes into groups, which may be predefined or data-driven, or organizing genes into a structure to represent some measure of distance between them. (pnas.org)
  • In a cluster analysis we start with raw data y , which we use to estimate the relative expression r of the genes among the mRNA samples. (pnas.org)
  • The simplest kind of clustering (case 1) assigns genes to prespecified groups. (pnas.org)
  • This is the case for our example below, where genes are clustered by calculating the correlation of an observed profile with a collection of fixed target profiles. (pnas.org)
  • contains all predicted genes from eleven virus families organized into ortholog groups by BLASTP similarity Skipredudant EMBOSS tool to remove redundant sequences from a set PISCES: A Protein Sequence Culling Server RDB90 UniRef: A non-redundant UniProt sequence database Uniclust: A clustered UniProtKB sequences at the level of 90%, 50% and 30% pairwise sequence identity. (wikipedia.org)
  • neural networks
  • the most well known unsupervised neural network is the self-organizing map and these models can usually be characterized as similar to one or more of the above models, and including subspace models when neural networks implement a form of Principal Component Analysis or Independent Component Analysis . (wikipedia.org)
  • statistically
  • We propose a bootstrap method to assess the reliability of clustering results in a statistically quantifiable manner. (pnas.org)
  • We identify statistically significant clusters with high or low rates in the zip code level using the Getis-Ord statistics. (hindawi.com)
  • optimal
  • The optimal number of clusters was chosen using a cross-validated likelihood method, which highlights the clustering pattern that generalizes best over the subjects. (dtu.dk)
  • The study of facility location problems, also known as location analysis, is a branch of operations research and computational geometry concerned with the optimal placement of facilities to minimize transportation costs while considering factors like avoiding placing hazardous materials near housing, and competitors' facilities. (wikipedia.org)
  • intervals
  • This study evaluates the clustering of hospitalization rates for stroke and compares this clustering with two different time intervals 2009-2010 and 2012-2013, corresponding to the beginning of the French National Stroke Plan 2010-2014. (hindawi.com)
  • methodology
  • It develops a methodology for clustering a large number of developing countries, identifying and ranking their welfare regimes, assessing their stability over the decade 1990-2000, and relating these to important structural variables. (bath.ac.uk)
  • objective
  • Cluster analysis as such is not an automatic task, but an iterative process of knowledge discovery or interactive multi-objective optimization that involves trial and failure. (wikipedia.org)
  • The objective of the clustering algorithm is to divide the given dataset (a set of points or objects) into groups of data instances or objects (or points) with distance or probabilistic measures. (oreilly.com)
  • The boundaries of these features appear fairly consistent across models when applying objective k-means clustering. (wikipedia.org)
  • depend
  • The appropriate clustering algorithm and parameter settings (including parameters such as the distance function to use, a density threshold or the number of expected clusters) depend on the individual data set and intended use of the results. (wikipedia.org)
  • Research
  • For example, when cluster analysis is performed as part of market research , specific groups can be identified within a population. (surveygizmo.com)
  • Hardware implementations of quantum annealing, such as the quantum annealing machines produced by D-Wave Systems [ 1 ], have been subject to multiple analyses in research, with the aim of characterizing the technology's usefulness for optimization, sampling, and clustering [ 2 - 17 ]. (frontiersin.org)
  • He worked for the Brain Research Laboratories (New York University) developing neurometric systems based on the multivariate statistical analysis of electroencephalographic signals (EEG). (wikipedia.org)
  • DAN publishes research results on a wide range of matters relating to diving safety and medicine and diving accident analysis, including annual reports on decompression illness and diving fatalities. (wikipedia.org)
  • displaystyle
  • These functions are both determined by finding the smallest cluster C {\displaystyle C} that contains both item i {\displaystyle i} and at least one larger-numbered item. (wikipedia.org)
  • Quantitative
  • Analysis of quantitative trait loci, or QTL, is a more recent addition to quantitative genetics, linking it more directly to molecular genetics. (wikipedia.org)
  • 1993
  • Alonso A, Martfn P, Albarran C, Sancho M (1993) Amplified fragment length polymorphism analysis of the VNTR locus D1S80 in central Spain. (springer.com)
  • Chistiakov DA, Gavrilov DK, Ovchinnikov IV, Nosikov W (1993) The use of PCR techniques for the VNTR allele distribution analysis of 120 unrelated russian individuals living in Moscow. (springer.com)
  • form
  • a clique , that is, a subset of nodes in a graph such that every two nodes in the subset are connected by an edge can be considered as a prototypical form of cluster. (wikipedia.org)
  • The output is displayed graphically, conveying the clustering and the underlying expression data simultaneously in a form intuitive for biologists. (pnas.org)
  • Clustering is a form of unsupervised machine learning, where instances are organized into groups whose members share similarities. (frontiersin.org)
  • Merge clusters (r) and (s) into a single cluster to form the next clustering m. (wikipedia.org)
  • The resulting motion forms small clusters of small plumes right above the core-mantle boundary that combine to form larger plumes and then contribute to superplumes. (wikipedia.org)
  • Workshop
  • During the 6th International Workshop on Compositional Data Analysis in June 2015, Vera was appointed president of a commission to formalize the creation of an international organization of scientists interested in the advancement and application of compositional data modeling. (wikipedia.org)