J Integr Bioinform - Clustering of gene expression profiles: creating initialization-independent clusterings by eliminating unstable genes.

Tópicos

{ method(1969) cluster(1462) data(1082) }
{ concept(1167) ontolog(924) domain(897) }
{ gene(2352) biolog(1181) express(1162) }
{ can(774) often(719) complex(702) }
{ first(2504) two(1366) second(1323) }
{ detect(2391) sensit(1101) algorithm(908) }
{ high(1669) rate(1365) level(1280) }
{ framework(1458) process(801) describ(734) }
{ group(2977) signific(1463) compar(1072) }
{ can(981) present(881) function(850) }
{ problem(2511) optim(1539) algorithm(950) }
{ ehr(2073) health(1662) electron(1139) }
{ activ(1138) subject(705) human(624) }
{ model(3404) distribut(989) bayesian(671) }
{ network(2748) neural(1063) input(814) }
{ assess(1506) score(1403) qualiti(1306) }
{ clinic(1479) use(1117) guidelin(835) }
{ extract(1171) text(1153) clinic(932) }
{ compound(1573) activ(1297) structur(1058) }
{ perform(1367) use(1326) method(1137) }
{ research(1218) medic(880) student(794) }
{ cost(1906) reduc(1198) effect(832) }
{ time(1939) patient(1703) rate(768) }
{ use(2086) technolog(871) perceiv(783) }
{ health(1844) social(1437) communiti(874) }
{ use(976) code(926) identifi(902) }
{ estim(2440) model(1874) function(577) }
{ process(1125) use(805) approach(778) }
{ imag(1947) propos(1133) code(1026) }
{ data(1737) use(1416) pattern(1282) }
{ inform(2794) health(2639) internet(1427) }
{ system(1976) rule(880) can(841) }
{ measur(2081) correl(1212) valu(896) }
{ imag(1057) registr(996) error(939) }
{ bind(1733) structur(1185) ligand(1036) }
{ sequenc(1873) structur(1644) protein(1328) }
{ method(1219) similar(1157) match(930) }
{ featur(3375) classif(2383) classifi(1994) }
{ imag(2830) propos(1344) filter(1198) }
{ imag(2675) segment(2577) method(1081) }
{ patient(2315) diseas(1263) diabet(1191) }
{ take(945) account(800) differ(722) }
{ studi(2440) review(1878) systemat(933) }
{ motion(1329) object(1292) video(1091) }
{ treatment(1704) effect(941) patient(846) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ error(1145) method(1030) estim(1020) }
{ chang(1828) time(1643) increas(1301) }
{ learn(2355) train(1041) set(1003) }
{ algorithm(1844) comput(1787) effici(935) }
{ method(1557) propos(1049) approach(1037) }
{ data(1714) softwar(1251) tool(1186) }
{ design(1359) user(1324) use(1319) }
{ control(1307) perform(991) simul(935) }
{ model(2220) cell(1177) simul(1124) }
{ care(1570) inform(1187) nurs(1089) }
{ general(901) number(790) one(736) }
{ method(984) reconstruct(947) comput(926) }
{ search(2224) databas(1162) retriev(909) }
{ featur(1941) imag(1645) propos(1176) }
{ case(1353) use(1143) diagnosi(1136) }
{ howev(809) still(633) remain(590) }
{ data(3963) clinic(1234) research(1004) }
{ studi(1410) differ(1259) use(1210) }
{ risk(3053) factor(974) diseas(938) }
{ perform(999) metric(946) measur(919) }
{ research(1085) discuss(1038) issu(1018) }
{ system(1050) medic(1026) inform(1018) }
{ import(1318) role(1303) understand(862) }
{ model(2341) predict(2261) use(1141) }
{ visual(1396) interact(850) tool(830) }
{ studi(1119) effect(1106) posit(819) }
{ blood(1257) pressur(1144) flow(957) }
{ spatial(1525) area(1432) region(1030) }
{ record(1888) medic(1808) patient(1693) }
{ health(3367) inform(1360) care(1135) }
{ model(3480) simul(1196) paramet(876) }
{ monitor(1329) mobil(1314) devic(1160) }
{ state(1844) use(1261) util(961) }
{ patient(2837) hospit(1953) medic(668) }
{ model(2656) set(1616) predict(1553) }
{ data(2317) use(1299) case(1017) }
{ age(1611) year(1155) adult(843) }
{ medic(1828) order(1363) alert(1069) }
{ signal(2180) analysi(812) frequenc(800) }
{ sampl(1606) size(1419) use(1276) }
{ data(3008) multipl(1320) sourc(1022) }
{ intervent(3218) particip(2042) group(1664) }
{ patient(1821) servic(1111) care(1106) }
{ analysi(2126) use(1163) compon(1037) }
{ structur(1116) can(940) graph(676) }
{ cancer(2502) breast(956) screen(824) }
{ use(1733) differ(960) four(931) }
{ drug(1928) target(777) effect(648) }
{ result(1111) use(1088) new(759) }
{ implement(1333) system(1263) develop(1122) }
{ survey(1388) particip(1329) question(1065) }
{ decis(3086) make(1611) patient(1517) }
{ activ(1452) weight(1219) physic(1104) }
{ method(2212) result(1239) propos(1039) }

Resumo

Clustering is an important approach in the analysis of biological data, and often a first step to identify interesting patterns of coexpression in gene expression data. Because of the high complexity and diversity of gene expression data, many genes cannot be easily assigned to a cluster, but even if the dissimilarity of these genes with all other gene groups is large, they will finally be forced to become member of a cluster. In this paper we show how to detect such elements, called unstable elements. We have developed an approach for iterative clustering algorithms in which unstable elements are deleted, making the iterative algorithm less dependent on initial centers. Although the approach is unsupervised, it is less likely that the clusters into which the reduced data set is subdivided contain false positives. This clustering yields a more differentiated approach for biological data, since the cluster analysis is divided into two parts: the pruned data set is divided into highly consistent clusters in an unsupervised way and the removed, unstable elements for which no meaningful cluster exists in unsupervised terms can be given a cluster with the use of biological knowledge and information about the likelihood of cluster membership. We illustrate our framework on both an artificial and real biological data set.

Resumo Limpo

cluster import approach analysi biolog data often first step identifi interest pattern coexpress gene express data high complex divers gene express data mani gene easili assign cluster even dissimilar gene gene group larg will final forc becom member cluster paper show detect element call unstabl element develop approach iter cluster algorithm unstabl element delet make iter algorithm less depend initi center although approach unsupervis less like cluster reduc data set subdivid contain fals posit cluster yield differenti approach biolog data sinc cluster analysi divid two part prune data set divid high consist cluster unsupervis way remov unstabl element meaning cluster exist unsupervis term can given cluster use biolog knowledg inform likelihood cluster membership illustr framework artifici real biolog data set

Resumos Similares

J Biomed Inform - Average correlation clustering algorithm (ACCA) for grouping of co-regulated genes with similar pattern of variation in their expression values. ( 0,81790155696236 )
Int J Health Geogr - A binary-based approach for detecting irregularly shaped clusters. ( 0,775717318887437 )
Brief. Bioinformatics - GO-function: deriving biologically relevant functions from statistically significant functions. ( 0,764254895779356 )
J. Comput. Biol. - Biological cluster evaluation for gene function prediction. ( 0,761936561954952 )
Int J Health Geogr - Detection of arbitrarily-shaped clusters using a neighbor-expanding approach: a case study on murine typhus in south Texas. ( 0,75639800417638 )
Spat Spatiotemporal Epidemiol - Optimal selection of the spatial scan parameters for cluster detection: a simulation study. ( 0,742174790122883 )
J Chem Inf Model - Metabolism site prediction based on xenobiotic structural formulas and PASS prediction algorithm. ( 0,734916619921922 )
Int J Health Geogr - Detecting activity locations from raw GPS data: a novel kernel-based algorithm. ( 0,732792693579554 )
IEEE Trans Pattern Anal Mach Intell - A Link-Based Approach to the Cluster Ensemble Problem. ( 0,706012600670744 )
Int J Health Geogr - Detection of clusters of a rare disease over a large territory: performance of cluster detection methods. ( 0,703904101664456 )
Med Decis Making - Developing appropriate methods for cost-effectiveness analysis of cluster randomized trials. ( 0,697227447134487 )
AMIA Annu Symp Proc - Using hierarchical mixture of experts model for fusion of outbreak detection methods. ( 0,690405776669652 )
IEEE Trans Neural Netw Learn Syst - Improved Fault Classification in Series Compensated Transmission Line: Comparative Evaluation of Chebyshev Neural Network Training Algorithms. ( 0,685164927399177 )
J Chem Inf Model - Investigation of the use of spectral clustering for the analysis of molecular data. ( 0,683623716320358 )
IEEE Trans Vis Comput Graph - GPU-based Multilevel Clustering. ( 0,682110826111262 )
Neural Comput - Spontaneous clustering via minimum -divergence. ( 0,679468983491503 )
Comput Biol Chem - Fast detection of high-order epistatic interactions in genome-wide association studies using information theoretic measure. ( 0,678743813917768 )
Brief. Bioinformatics - Accounting for noise when clustering biological data. ( 0,67080882109621 )
J Biomed Inform - Enabling enrichment analysis with the Human Disease Ontology. ( 0,67004998887925 )
Comput. Biol. Med. - Multi-stage filtering for improving confidence level and determining dominant clusters in clustering algorithms of gene expression data. ( 0,664825956688394 )
J Chem Inf Model - Comparison of combinatorial clustering methods on pharmacological data sets represented by machine learning-selected real molecular descriptors. ( 0,663559074806482 )
J Biomed Inform - Statistical file matching of flow cytometry data. ( 0,661112151188315 )
Med Decis Making - Multiple imputation methods for handling missing data in cost-effectiveness analyses that use data from hierarchical studies: an application to cluster randomized trials. ( 0,659071641065362 )
IEEE Trans Pattern Anal Mach Intell - Semi-Supervised Kernel Mean Shift Clustering. ( 0,655084159631534 )
J. Comput. Biol. - A geometric clustering algorithm with applications to structural data. ( 0,651605396051689 )
Comput Methods Programs Biomed - Fuzzy and hard clustering analysis for thyroid disease. ( 0,65048404713605 )
IEEE J Biomed Health Inform - Red blood cell cluster separation from digital images for use in sickle cell disease. ( 0,648401798437456 )
J Med Syst - Application of attribute weighting method based on clustering centers to discrimination of linearly non-separable medical datasets. ( 0,645789454583718 )
Comput Biol Chem - Mode of action classification of chemicals using multi-concentration time-dependent cellular response profiles. ( 0,645698122216534 )
AMIA Annu Symp Proc - A fast algorithm for learning epistatic genomic relationships. ( 0,643209245435375 )
J Integr Bioinform - An evolutionary and visual framework for clustering of DNA microarray data. ( 0,630213249254565 )
J Chem Inf Model - Consensus methods for combining multiple clusterings of chemical structures. ( 0,629596332429795 )
J Am Med Inform Assoc - Leveraging electronic healthcare record standards and semantic web technologies for the identification of patient cohorts. ( 0,629351397947779 )
Comput Math Methods Med - A wavelet relational fuzzy C-means algorithm for 2D gel image segmentation. ( 0,624788216846843 )
J. Med. Internet Res. - Security analysis and improvements to the PsychoPass method. ( 0,620719748913412 )
Comput. Biol. Med. - Evaluation of automatic feature detection algorithms in EEG: application to interburst intervals. ( 0,61217815352413 )
Neural Comput - A nonparametric clustering algorithm with a quantile-based likelihood estimator. ( 0,611204318264652 )
Int J Neural Syst - A cluster merging method for time series microarray with production values. ( 0,610845862394254 )
AMIA Annu Symp Proc - Automatic selection of preprocessing methods for improving predictions on mass spectrometry protein profiles. ( 0,610532646542652 )
Comput Math Methods Med - Novel harmonic regularization approach for variable selection in Cox's proportional hazards model. ( 0,60952151556737 )
Int J Comput Assist Radiol Surg - CT dataset anisotropy management for oral implantology planning software. ( 0,607525473889432 )
J Biomed Inform - Algorithmic and user study of an autocompletion algorithm on a large medical vocabulary. ( 0,607077279148921 )
Artif Intell Med - Vicinal support vector classifier using supervised kernel-based clustering. ( 0,606422739828242 )
Comput. Biol. Med. - CAM: a web tool for combining array CGH and microarray gene expression data from multiple samples. ( 0,605936692619941 )
J Biomed Inform - A semantic framework to protect the privacy of electronic health records with non-numerical attributes. ( 0,605881895186771 )
J Am Med Inform Assoc - Privacy-preserving heterogeneous health data sharing. ( 0,604053846878724 )
AMIA Annu Symp Proc - Crowdsourcing the verification of relationships in biomedical ontologies. ( 0,601835085362606 )
Artif Intell Med - Weighted spherical 1-mean with phase shift and its application in electrocardiogram discord detection. ( 0,600845791813523 )
Comput Math Methods Med - Decimative spectral estimation with unconstrained model order. ( 0,600255372308591 )
Sci Data - Assessment of lipidomic species in hepatocyte lipid droplets from stressed mouse models. ( 0,597785834908172 )
Comput Math Methods Med - A robust rerank approach for feature selection and its application to pooling-based GWA studies. ( 0,594975884678858 )
Int J Health Geogr - Using statistical methods and genotyping to detect tuberculosis outbreaks. ( 0,594392237786349 )
Comput Math Methods Med - White blood cell segmentation by circle detection using electromagnetism-like optimization. ( 0,593468894351978 )
Comput. Biol. Med. - Analysis of adductors angle measurement in Hammersmith infant neurological examinations using mean shift segmentation and feature point based object tracking. ( 0,593331839562829 )
J Biomed Inform - Extension of the survival dimensionality reduction algorithm to detect epistasis in competing risks models (SDR-CR). ( 0,593248568983348 )
Comput Methods Programs Biomed - OLYMPUS: an automated hybrid clustering method in time series gene expression. Case study: host response after Influenza A (H1N1) infection. ( 0,59309363853775 )
J. Comput. Biol. - EDAR: an efficient error detection and removal algorithm for next generation sequencing data. ( 0,590143554255506 )
Comput. Biol. Med. - Nonlinear dimensionality reduction of gene expression data for visualization and clustering analysis of cancer tissue samples. ( 0,589164064242879 )
Med Biol Eng Comput - Detection of swallows with silent aspiration using swallowing and breath sound analysis. ( 0,588101626025505 )
Comput Methods Programs Biomed - fMRI analysis on the GPU-possibilities and challenges. ( 0,586244582387973 )
Int J Neural Syst - A genetic graph-based approach for partitional clustering. ( 0,585372331906499 )
AMIA Annu Symp Proc - Dissimilarities in the Logical Modeling of Apparently Similar Concepts in SNOMED CT. ( 0,584994673001393 )
Comput. Biol. Med. - A straightforward approach to computer-aided polyp detection using a polyp-specific volumetric feature in CT colonography. ( 0,582650965815882 )
Comput Biol Chem - Meta-analysis of microarray data: The case of imatinib resistance in chronic myelogenous leukemia. ( 0,581463713411938 )
BMC Med Inform Decis Mak - Efficient algorithms for fast integration on large data sets from multiple sources. ( 0,580202028200392 )
J Biomed Inform - Quantifying the determinants of outbreak detection performance through simulation and machine learning. ( 0,579569886016231 )
Comput. Biol. Med. - A methodology to identify consensus classes from clustering algorithms applied to immunohistochemical data from breast cancer patients. ( 0,576789220369238 )
Comput Math Methods Med - A new particle swarm optimization-based method for phase unwrapping of MRI data. ( 0,576583365681946 )
Comput. Aided Surg. - The Equidistant Method - a novel hip joint simulation algorithm for detection of femoroacetabular impingement. ( 0,572665359711535 )
Comput. Biol. Med. - Alpha-plane based automatic general type-2 fuzzy clustering based on simulated annealing meta-heuristic algorithm for analyzing gene expression data. ( 0,571501979751247 )
IEEE Trans Image Process - Linear discriminant analysis based on L1-norm maximization. ( 0,571429191145149 )
Spat Spatiotemporal Epidemiol - Performance of cancer cluster Q-statistics for case-control residential histories. ( 0,569804282991852 )
Artif Intell Med - Missing data imputation using statistical and machine learning methods in a real breast cancer problem. ( 0,568051416617728 )
Comput Math Methods Med - Feature selection for better identification of subtypes of Guillain-Barr? syndrome. ( 0,567364174913158 )
Brief. Bioinformatics - A quantitative model of transcriptional differentiation driving host-pathogen interactions. ( 0,567182199715186 )
Brief. Bioinformatics - Similarity of markers identified from cancer gene expression studies: observations from GEO. ( 0,56567301045705 )
Comput Methods Programs Biomed - Improvements on a privacy-protection algorithm for DNA sequences with generalization lattices. ( 0,564658323532557 )
J. Comput. Biol. - Markov logic networks in the analysis of genetic data. ( 0,561872262589837 )
Brief. Bioinformatics - A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis. ( 0,560913404911746 )
Int J Neural Syst - Adaptive k-means algorithm for overlapped graph clustering. ( 0,559914406459171 )
Comput Methods Programs Biomed - Development and application of efficient pathway enumeration algorithms for metabolic engineering applications. ( 0,559002743423203 )
Comput Biol Chem - Ped_Outlier software for automatic identification of within-family outliers. ( 0,558532265895882 )
Comput Math Methods Med - Recent progress on the factorization method for electrical impedance tomography. ( 0,558280484229814 )
Methods Inf Med - Application of microarray analysis on computer cluster and cloud platforms. ( 0,551529501260324 )
IEEE Trans Image Process - Self-adaptively Weighted Co-saliency Detection via Rank Constraint. ( 0,549389956841192 )
J Biomed Inform - A machine-learned knowledge discovery method for associating complex phenotypes with complex genotypes. Application to pain. ( 0,547366987924031 )
Brief. Bioinformatics - Travelling the world of gene-gene interactions. ( 0,547328505241366 )
J Chem Inf Model - Benchmark data sets for structure-based computational target prediction. ( 0,546647486608823 )
Methods Inf Med - A database de-identification framework to enable direct queries on medical data for secondary use. ( 0,545234829769125 )
Artif Intell Med - A knowledge-driven approach to biomedical document conceptualization. ( 0,543476757697109 )
Med Decis Making - Cost-saving tree-structured survival analysis for hip fracture of study of osteoporotic fractures data. ( 0,541818283575416 )
IEEE Trans Image Process - Enhancing Low-Rank Subspace Clustering by Manifold Regularization. ( 0,541507237713011 )
IEEE Trans Pattern Anal Mach Intell - A Minimum Volume Covering Approach With a Set of Ellipsoids. ( 0,540707520606369 )
Int J Comput Assist Radiol Surg - Preclinical feasibility of a technology framework for MRI-guided iliac angioplasty. ( 0,539105420727523 )
AMIA Annu Symp Proc - Using ontology network structure in text mining. ( 0,538056840684725 )
Artif Intell Med - Multi-test decision tree and its application to microarray data classification. ( 0,537361961295212 )
Comput Math Methods Med - Liver segmentation based on Snakes Model and improved GrowCut algorithm in abdominal CT image. ( 0,537148927000628 )
Int J Health Geogr - Interactive web-based mapping: bridging technology and data for health. ( 0,534953474151051 )
AMIA Annu Symp Proc - Patient clustering with uncoded text in electronic medical records. ( 0,534908544679741 )
Int J Health Geogr - Voronoi distance based prospective space-time scans for point data sets: a dengue fever cluster analysis in a southeast Brazilian town. ( 0,534777010082404 )