Comput Biol Chem - GPEC: a Cytoscape plug-in for random walk-based gene prioritization and biomedical evidence collection.

Tópicos

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

Resumo

Finding genes associated with a disease is an important issue in the biomedical area and many gene prioritization methods have been proposed for this goal. Among these, network-based approaches are recently proposed and outperformed functional annotation-based ones. Here, we introduce a novel Cytoscape plug-in, GPEC, to help identify putative genes likely to be associated with specific diseases or pathways. In the plug-in, gene prioritization is performed through a random walk with restart algorithm, a state-of-the art network-based method, along with a gene/protein relationship network. The plug-in also allows users efficiently collect biomedical evidence for highly ranked candidate genes. A set of known genes, candidate genes and a gene/protein relationship network can be provided in a flexible way.

Resumo Limpo

find gene associ diseas import issu biomed area mani gene priorit method propos goal among networkbas approach recent propos outperform function annotationbas one introduc novel cytoscap plugin gpec help identifi putat gene like associ specif diseas pathway plugin gene priorit perform random walk restart algorithm stateofth art networkbas method along geneprotein relationship network plugin also allow user effici collect biomed evid high rank candid gene set known gene candid gene geneprotein relationship network can provid flexibl way

Resumos Similares

J Am Med Inform Assoc - Extracting coordinated patterns of DNA methylation and gene expression in ovarian cancer. ( 0,885424908336172 )
Comput Math Methods Med - First comprehensive in silico analysis of the functional and structural consequences of SNPs in human GalNAc-T1 gene. ( 0,867758026784865 )
Brief. Bioinformatics - Revealing the architecture of genetic and epigenetic regulation: a maximum likelihood model. ( 0,864330879727346 )
J. Comput. Biol. - Bioinformatics method to analyze the mechanism of pancreatic cancer disorder. ( 0,859726615241768 )
Comput. Biol. Med. - Identification and analysis of the regulatory network of Myc and microRNAs from high-throughput experimental data. ( 0,856756871087902 )
Wiley Interdiscip Rev Syst Biol Med - Signaling networks in palate development. ( 0,853460717751752 )
J Biomed Inform - Comparative analysis of a novel disease phenotype network based on clinical manifestations. ( 0,852629271493031 )
Wiley Interdiscip Rev Syst Biol Med - Diverse functional networks of Tbx3 in development and disease. ( 0,85183009721914 )
J. Comput. Biol. - Computational disease gene prioritization: an appraisal. ( 0,85170452375792 )
J. Comput. Biol. - A topology-based score for pathway enrichment. ( 0,850708304513037 )
Brief. Bioinformatics - Identifying miRNAs, targets and functions. ( 0,849883412421193 )
J. Comput. Biol. - An algorithm for efficient identification of branched metabolic pathways. ( 0,849715239067529 )
J Integr Bioinform - Towards prediction and prioritization of disease genes by the modularity of human phenome-genome assembled network. ( 0,848890722801255 )
Artif Intell Med - An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods. ( 0,845820270287945 )
J Integr Bioinform - An integrative bioinformatics framework for genome-scale multiple level network reconstruction of rice. ( 0,845176606301332 )
Comput Biol Chem - Disruption of murine Tcte3-3 induces tissue specific apoptosis via co-expression of Anxa5 and Pebp1. ( 0,842299027624909 )
J Am Med Inform Assoc - Identifying disease genes and module biomarkers by differential interactions. ( 0,841910362779985 )
Brief. Bioinformatics - Identification of aberrant pathways and network activities from high-throughput data. ( 0,83969835570033 )
Comput Math Methods Med - Integrating gene expression and protein interaction data for signaling pathway prediction of Alzheimer's disease. ( 0,839115527374744 )
Wiley Interdiscip Rev Syst Biol Med - Integrating omics into the cardiac differentiation of human pluripotent stem cells. ( 0,838280342821888 )
J Integr Bioinform - Knowledge enrichment analysis for human tissue-specific genes uncover new biological insights. ( 0,837672181699246 )
Artif Intell Med - Identifying regulatory relationships among genomic loci, biological pathways, and disease. ( 0,836705603536367 )
Comput. Biol. Med. - Mathematical modeling and sensitivity analysis of the integrated TNFa-mediated apoptotic pathway for identifying key regulators. ( 0,836369109002539 )
Comput Math Methods Med - Understanding the pathogenesis of Kawasaki disease by network and pathway analysis. ( 0,835928789946027 )
Wiley Interdiscip Rev Syst Biol Med - Recent advances in prostate development and links to prostatic diseases. ( 0,834044613323042 )
Comput Biol Chem - Identifying novel prostate cancer associated pathways based on integrative microarray data analysis. ( 0,831856900442704 )
Comput. Biol. Med. - A review on the computational approaches for gene regulatory network construction. ( 0,830854853933761 )
Wiley Interdiscip Rev Syst Biol Med - miRNA regulation in the context of functional protein networks: principles and applications. ( 0,830771331331259 )
Sci Data - DNA methylation temporal profiling following peripheral versus central nervous system axotomy. ( 0,83070262891641 )
J. Comput. Biol. - Vavien: an algorithm for prioritizing candidate disease genes based on topological similarity of proteins in interaction networks. ( 0,83055476568856 )
J Integr Bioinform - Assembling cell context-specific gene sets: a case in cardiomyopathy. ( 0,830066179591605 )
Comput Biol Chem - In silico analysis of cis-acting regulatory elements in 5' regulatory regions of sucrose transporter gene families in rice (Oryza sativa Japonica) and Arabidopsis thaliana. ( 0,829159498622387 )
J Biomed Inform - A comparative study of covariance selection models for the inference of gene regulatory networks. ( 0,823230246407276 )
Brief. Bioinformatics - Learning transcriptional regulation on a genome scale: a theoretical analysis based on gene expression data. ( 0,822368216591636 )
Comput. Biol. Med. - Degrees of separation as a statistical tool for evaluating candidate genes. ( 0,820944456736817 )
Wiley Interdiscip Rev Syst Biol Med - Postgenomic technologies targeting the Wnt signaling network. ( 0,819538954334579 )
Wiley Interdiscip Rev Syst Biol Med - Using variability in gene expression as a tool for studying gene regulation. ( 0,81899022318545 )
Comput Biol Chem - Using volcano plots and regularized-chi statistics in genetic association studies. ( 0,818862175714404 )
IEEE J Biomed Health Inform - Using evolutional properties of gene networks in understanding survival prognosis of glioblastoma. ( 0,81834099881052 )
J Integr Bioinform - A study of the short and long-term regulation of E. coli metabolic pathways. ( 0,817889305749467 )
Wiley Interdiscip Rev Syst Biol Med - Systems biology of adipose tissue metabolism: regulation of growth, signaling and inflammation. ( 0,817856623403479 )
Comput Biol Chem - Exploring the complexity of pathway-drug relationships using latent Dirichlet allocation. ( 0,817671102828372 )
J Integr Bioinform - Network expansion and pathway enrichment analysis towards biologically significant findings from microarrays. ( 0,817295971357601 )
Curr Protoc Bioinformatics - BEDTools: The Swiss-Army Tool for Genome Feature Analysis. ( 0,815179532086028 )
J Am Med Inform Assoc - Knowledge boosting: a graph-based integration approach with multi-omics data and genomic knowledge for cancer clinical outcome prediction. ( 0,813332415428757 )
Wiley Interdiscip Rev Syst Biol Med - Network biology: a direct approach to study biological function. ( 0,813329822423894 )
Comput Biol Chem - Using gene expression programming to infer gene regulatory networks from time-series data. ( 0,811069284191176 )
J Am Med Inform Assoc - An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer. ( 0,810436105874218 )
Wiley Interdiscip Rev Syst Biol Med - Stem cell bioengineering at the interface of systems-based models and high-throughput platforms. ( 0,808447856287161 )
J Am Med Inform Assoc - Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseases. ( 0,806278461021106 )
J Biomed Inform - Independent component analysis: mining microarray data for fundamental human gene expression modules. ( 0,804563760694738 )
J Biomed Inform - Prioritization of potential candidate disease genes by topological similarity of protein-protein interaction network and phenotype data. ( 0,803202577390757 )
Comput Biol Chem - Expression patterns of photoperiod and temperature regulated heading date genes in Oryza sativa. ( 0,802779722321299 )
Brief. Bioinformatics - Apoptosis regulatory protein-protein interaction demonstrates hierarchical scale-free fractal network. ( 0,802022783380168 )
J Biomed Inform - Gene pathways and subnetworks distinguish between major glioma subtypes and elucidate potential underlying biology. ( 0,801623884315537 )
J Biomed Inform - The detection of risk pathways, regulated by miRNAs, via the integration of sample-matched miRNA-mRNA profiles and pathway structure. ( 0,800941849822368 )
Methods Inf Med - Pathway based microarray analysis, utilising enzyme compounds and cascade events. ( 0,800273132850263 )
J Am Med Inform Assoc - Complex-disease networks of trait-associated single-nucleotide polymorphisms (SNPs) unveiled by information theory. ( 0,798111210757731 )
AMIA Annu Symp Proc - An ontology-neutral framework for enrichment analysis. ( 0,79785798101467 )
Brief. Bioinformatics - Targeted metabolic reconstruction: a novel approach for the characterization of plant-pathogen interactions. ( 0,797794810189942 )
Comput Biol Chem - Large-scale mining co-expressed genes in Arabidopsis anther: from pair to group. ( 0,79717561703528 )
J Biomed Inform - Protein interaction network underpins concordant prognosis among heterogeneous breast cancer signatures. ( 0,796230700572389 )
Wiley Interdiscip Rev Syst Biol Med - Regulatory variation: an emerging vantage point for cancer biology. ( 0,795771144774865 )
Brief. Bioinformatics - How to cluster gene expression dynamics in response to environmental signals. ( 0,795393447600665 )
Comput. Biol. Med. - Revealing pathway maps of renal cell carcinoma by gene expression change. ( 0,794647939627873 )
Methods Inf Med - Identification of breast cancer prognosis markers using integrative sparse boosting. ( 0,793702677862463 )
Wiley Interdiscip Rev Syst Biol Med - Reverse-engineering human regulatory networks. ( 0,793252062212364 )
J Biomed Inform - Hemojuvelin-hepcidin axis modeled and analyzed using Petri nets. ( 0,789439222305483 )
Wiley Interdiscip Rev Syst Biol Med - Engineered genetic information processing circuits. ( 0,789292263009054 )
Comput Biol Chem - A computational method of predicting regulatory interactions in Arabidopsis based on gene expression data and sequence information. ( 0,78913345774693 )
AMIA Annu Symp Proc - Mining disease fingerprints from within genetic pathways. ( 0,786717588576325 )
Wiley Interdiscip Rev Syst Biol Med - Cyclic nucleotide signaling in intestinal epithelia: getting to the gut of the matter. ( 0,786303035452879 )
Comput Methods Programs Biomed - TMT-HCC: a tool for text mining the biomedical literature for hepatocellular carcinoma (HCC) biomarkers identification. ( 0,785980306992448 )
J Integr Bioinform - Uncovering the expression patterns of chimeric transcripts using surveys of affymetrix GeneChips. ( 0,785941931858426 )
Wiley Interdiscip Rev Syst Biol Med - Using a systems biology approach to understand and study the mechanisms of metastasis. ( 0,784959379629735 )
J Am Med Inform Assoc - Utility of gene-specific algorithms for predicting pathogenicity of uncertain gene variants. ( 0,784783881176796 )
J Biomed Inform - Inferring cell cycle feedback regulation from gene expression data. ( 0,784254384211181 )
Int J Med Inform - Translating genome wide association study results to associations among common diseases: in silico study with an electronic medical record. ( 0,783999138897462 )
Wiley Interdiscip Rev Syst Biol Med - Genome-wide approaches in the study of microRNA biology. ( 0,782348422010021 )
Comput Biol Chem - Bioinformatic analysis of molecular network of glucosinolate biosynthesis. ( 0,781015728012901 )
Brief. Bioinformatics - Toward microRNA-mediated gene regulatory networks in plants. ( 0,780768658185509 )
Comput Biol Chem - Revealing weak differential gene expressions and their reproducible functions associated with breast cancer metastasis. ( 0,780768655651749 )
J Biomed Inform - The inference of breast cancer metastasis through gene regulatory networks. ( 0,778220736591264 )
Comput Biol Chem - Analysis of transcriptional synergy between upstream regions and introns in ribosomal protein genes of yeast. ( 0,777789655784808 )
Comput Biol Chem - Statistical analysis of combinatorial transcriptional regulatory motifs in human intron-containing promoter sequences. ( 0,774566865295396 )
Wiley Interdiscip Rev Syst Biol Med - Sex and the circuitry: progress toward a systems-level understanding of vertebrate sex determination. ( 0,774463246703258 )
J Integr Bioinform - Reconstruction of biological networks based on life science data integration. ( 0,773638968481375 )
Wiley Interdiscip Rev Syst Biol Med - Noncoding RNAs in gene regulation. ( 0,771884160734707 )
J Integr Bioinform - Predicting breast cancer chemotherapeutic response using a novel tool for microarray data analysis. ( 0,771759694083885 )
Wiley Interdiscip Rev Syst Biol Med - Protein microarrays for genome-wide posttranslational modification analysis. ( 0,771294868667702 )
Comput Biol Chem - Gene expression patterns combined with bioinformatics analysis identify genes associated with cholangiocarcinoma. ( 0,771193457378611 )
Wiley Interdiscip Rev Syst Biol Med - Bioimage informatics for understanding spatiotemporal dynamics of cellular processes. ( 0,770999075066553 )
AMIA Annu Symp Proc - Towards mechanism classifiers: expression-anchored Gene Ontology signature predicts clinical outcome in lung adenocarcinoma patients. ( 0,770685443900507 )
Wiley Interdiscip Rev Syst Biol Med - Genome network medicine: innovation to overcome huge challenges in cancer therapy. ( 0,768628382436805 )
Wiley Interdiscip Rev Syst Biol Med - The zebrafish: scalable in vivo modeling for systems biology. ( 0,768192331347145 )
Comput. Biol. Med. - A molecular prospective provides new insights into implication of PDYN and OPRK1 genes in alcohol dependence. ( 0,767358648314476 )
J Biomed Inform - Systems-based biological concordance and predictive reproducibility of gene set discovery methods in cardiovascular disease. ( 0,767358648314476 )
J Integr Bioinform - Profiling of genetic switches using boolean implications in expression data. ( 0,765726388749917 )
Wiley Interdiscip Rev Syst Biol Med - Where gene discovery turns into systems biology: genome-scale RNAi screens in Drosophila. ( 0,765616843483346 )
Wiley Interdiscip Rev Syst Biol Med - The adaptor protein LAT serves as an integration node for signaling pathways that drive T cell activation. ( 0,765354488874185 )