Comput Biol Chem - Using volcano plots and regularized-chi statistics in genetic association studies.

Tópicos

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

Resumo

Labor intensive experiments are typically required to identify the causal disease variants from a list of disease associated variants in the genome. For designing such experiments, candidate variants are ranked by their strength of genetic association with the disease. However, the two commonly used measures of genetic association, the odds-ratio (OR) and p-value may rank variants in different order. To integrate these two measures into a single analysis, here we transfer the volcano plot methodology from gene expression analysis to genetic association studies. In its original setting, volcano plots are scatter plots of fold-change and t-test statistic (or -log of the p-value), with the latter being more sensitive to sample size. In genetic association studies, the OR and Pearson's chi-square statistic (or equivalently its square root, chi; or the standardized log(OR)) can be analogously used in a volcano plot, allowing for their visual inspection. Moreover, the geometric interpretation of these plots leads to an intuitive method for filtering results by a combination of both OR and chi-square statistic, which we term "regularized-chi". This method selects associated markers by a smooth curve in the volcano plot instead of the right-angled lines which corresponds to independent cutoffs for OR and chi-square statistic. The regularized-chi incorporates relatively more signals from variants with lower minor-allele-frequencies than chi-square test statistic. As rare variants tend to have stronger functional effects, regularized-chi is better suited to the task of prioritization of candidate genes.

Resumo Limpo

labor intens experi typic requir identifi causal diseas variant list diseas associ variant genom design experi candid variant rank strength genet associ diseas howev two common use measur genet associ oddsratio pvalu may rank variant differ order integr two measur singl analysi transfer volcano plot methodolog gene express analysi genet associ studi origin set volcano plot scatter plot foldchang ttest statist log pvalu latter sensit sampl size genet associ studi pearson chisquar statist equival squar root chi standard logor can analog use volcano plot allow visual inspect moreov geometr interpret plot lead intuit method filter result combin chisquar statist term regularizedchi method select associ marker smooth curv volcano plot instead rightangl line correspond independ cutoff chisquar statist regularizedchi incorpor relat signal variant lower minorallelefrequ chisquar test statist rare variant tend stronger function effect regularizedchi better suit task priorit candid gene

Resumos Similares

J. Comput. Biol. - A topology-based score for pathway enrichment. ( 0,906109788020833 )
J Biomed Inform - Comparative analysis of a novel disease phenotype network based on clinical manifestations. ( 0,884212308929083 )
Brief. Bioinformatics - Revealing the architecture of genetic and epigenetic regulation: a maximum likelihood model. ( 0,881357137408817 )
Comput. Biol. Med. - Degrees of separation as a statistical tool for evaluating candidate genes. ( 0,879486322669616 )
J Am Med Inform Assoc - Identifying disease genes and module biomarkers by differential interactions. ( 0,875086795120857 )
J Integr Bioinform - Network expansion and pathway enrichment analysis towards biologically significant findings from microarrays. ( 0,872604259893162 )
J Biomed Inform - Prioritization of potential candidate disease genes by topological similarity of protein-protein interaction network and phenotype data. ( 0,870528244940077 )
J. Comput. Biol. - Bioinformatics method to analyze the mechanism of pancreatic cancer disorder. ( 0,869179252884491 )
J Integr Bioinform - An integrative bioinformatics framework for genome-scale multiple level network reconstruction of rice. ( 0,868950384212889 )
J Integr Bioinform - Towards prediction and prioritization of disease genes by the modularity of human phenome-genome assembled network. ( 0,86830137414545 )
Comput Biol Chem - Identifying novel prostate cancer associated pathways based on integrative microarray data analysis. ( 0,864881464247322 )
J Am Med Inform Assoc - Extracting coordinated patterns of DNA methylation and gene expression in ovarian cancer. ( 0,862510585293027 )
Wiley Interdiscip Rev Syst Biol Med - Diverse functional networks of Tbx3 in development and disease. ( 0,860333834701928 )
Comput. Biol. Med. - Identification and analysis of the regulatory network of Myc and microRNAs from high-throughput experimental data. ( 0,858976560716654 )
Comput Biol Chem - Disruption of murine Tcte3-3 induces tissue specific apoptosis via co-expression of Anxa5 and Pebp1. ( 0,858566805814886 )
Wiley Interdiscip Rev Syst Biol Med - Using variability in gene expression as a tool for studying gene regulation. ( 0,857789594167364 )
Wiley Interdiscip Rev Syst Biol Med - Using a systems biology approach to understand and study the mechanisms of metastasis. ( 0,857612127853171 )
J Am Med Inform Assoc - Advantages of genomic complexity: bioinformatics opportunities in microRNA cancer signatures. ( 0,85744713047495 )
Artif Intell Med - Identifying regulatory relationships among genomic loci, biological pathways, and disease. ( 0,8564740394161 )
J. Comput. Biol. - An algorithm for efficient identification of branched metabolic pathways. ( 0,856226771478466 )
Comput Math Methods Med - First comprehensive in silico analysis of the functional and structural consequences of SNPs in human GalNAc-T1 gene. ( 0,85607686855403 )
J Am Med Inform Assoc - An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer. ( 0,855667398272144 )
Artif Intell Med - An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods. ( 0,851356101282494 )
J Am Med Inform Assoc - Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseases. ( 0,851281482236724 )
J. Comput. Biol. - Vavien: an algorithm for prioritizing candidate disease genes based on topological similarity of proteins in interaction networks. ( 0,850423909404361 )
J. Comput. Biol. - Computational disease gene prioritization: an appraisal. ( 0,849964977616206 )
J Integr Bioinform - Assembling cell context-specific gene sets: a case in cardiomyopathy. ( 0,848249313110324 )
Comput Math Methods Med - Integrating gene expression and protein interaction data for signaling pathway prediction of Alzheimer's disease. ( 0,847986974778108 )
J Integr Bioinform - Knowledge enrichment analysis for human tissue-specific genes uncover new biological insights. ( 0,847699367316006 )
J Am Med Inform Assoc - Complex-disease networks of trait-associated single-nucleotide polymorphisms (SNPs) unveiled by information theory. ( 0,847059152299354 )
Comput Biol Chem - Bioinformatic analysis of molecular network of glucosinolate biosynthesis. ( 0,84635899397018 )
Brief. Bioinformatics - Identifying miRNAs, targets and functions. ( 0,845783743078585 )
J Biomed Inform - Gene pathways and subnetworks distinguish between major glioma subtypes and elucidate potential underlying biology. ( 0,844065912898894 )
Comput Math Methods Med - Understanding the pathogenesis of Kawasaki disease by network and pathway analysis. ( 0,843931925770489 )
Comput. Biol. Med. - Mathematical modeling and sensitivity analysis of the integrated TNFa-mediated apoptotic pathway for identifying key regulators. ( 0,840899898665934 )
Wiley Interdiscip Rev Syst Biol Med - Signaling networks in palate development. ( 0,839279998970553 )
Comput Biol Chem - Using gene expression programming to infer gene regulatory networks from time-series data. ( 0,839112569820938 )
Wiley Interdiscip Rev Syst Biol Med - Systems biology of adipose tissue metabolism: regulation of growth, signaling and inflammation. ( 0,839094036048317 )
Comput Biol Chem - Expression patterns of photoperiod and temperature regulated heading date genes in Oryza sativa. ( 0,836708836317203 )
Wiley Interdiscip Rev Syst Biol Med - Network biology: a direct approach to study biological function. ( 0,836157678829505 )
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. ( 0,835964556626744 )
Brief. Bioinformatics - Targeted metabolic reconstruction: a novel approach for the characterization of plant-pathogen interactions. ( 0,835713865469705 )
Wiley Interdiscip Rev Syst Biol Med - miRNA regulation in the context of functional protein networks: principles and applications. ( 0,834708257267644 )
Sci Data - DNA methylation temporal profiling following peripheral versus central nervous system axotomy. ( 0,834334132933653 )
Methods Inf Med - Pathway based microarray analysis, utilising enzyme compounds and cascade events. ( 0,834101908634037 )
AMIA Annu Symp Proc - An ontology-neutral framework for enrichment analysis. ( 0,833860684633836 )
Wiley Interdiscip Rev Syst Biol Med - Integrating omics into the cardiac differentiation of human pluripotent stem cells. ( 0,832114767427555 )
J Am Med Inform Assoc - Knowledge boosting: a graph-based integration approach with multi-omics data and genomic knowledge for cancer clinical outcome prediction. ( 0,830560103260754 )
J Biomed Inform - Independent component analysis: mining microarray data for fundamental human gene expression modules. ( 0,829558601379148 )
J Biomed Inform - A comparative study of covariance selection models for the inference of gene regulatory networks. ( 0,828796815749528 )
J Integr Bioinform - Profiling of genetic switches using boolean implications in expression data. ( 0,828516967611365 )
Comput Biol Chem - Statistical analysis of combinatorial transcriptional regulatory motifs in human intron-containing promoter sequences. ( 0,828196495322211 )
AMIA Annu Symp Proc - Mining disease fingerprints from within genetic pathways. ( 0,826386989189682 )
Comput Biol Chem - GPEC: a Cytoscape plug-in for random walk-based gene prioritization and biomedical evidence collection. ( 0,818862175714404 )
Wiley Interdiscip Rev Syst Biol Med - Recent advances in prostate development and links to prostatic diseases. ( 0,818489192210824 )
J Integr Bioinform - A study of the short and long-term regulation of E. coli metabolic pathways. ( 0,818108887617366 )
Wiley Interdiscip Rev Syst Biol Med - Regulatory variation: an emerging vantage point for cancer biology. ( 0,818073939638441 )
Brief. Bioinformatics - Learning transcriptional regulation on a genome scale: a theoretical analysis based on gene expression data. ( 0,817933361481411 )
Brief. Bioinformatics - Identification of aberrant pathways and network activities from high-throughput data. ( 0,815858145068301 )
J Biomed Inform - The detection of risk pathways, regulated by miRNAs, via the integration of sample-matched miRNA-mRNA profiles and pathway structure. ( 0,815772950108703 )
Comput Biol Chem - Meta-analysis of microarray data: The case of imatinib resistance in chronic myelogenous leukemia. ( 0,815020858289854 )
Wiley Interdiscip Rev Syst Biol Med - Postgenomic technologies targeting the Wnt signaling network. ( 0,814226741193404 )
Comput. Biol. Med. - Revealing pathway maps of renal cell carcinoma by gene expression change. ( 0,813457665932949 )
Comput. Biol. Med. - Nonlinear dimensionality reduction of gene expression data for visualization and clustering analysis of cancer tissue samples. ( 0,807319699087345 )
J. Comput. Biol. - A stationary wavelet entropy-based clustering approach accurately predicts gene expression. ( 0,80487833344715 )
IEEE J Biomed Health Inform - Using evolutional properties of gene networks in understanding survival prognosis of glioblastoma. ( 0,803923028118277 )
Brief. Bioinformatics - Combining multidimensional genomic measurements for predicting cancer prognosis: observations from TCGA. ( 0,80386013363222 )
J Biomed Inform - Systems-based biological concordance and predictive reproducibility of gene set discovery methods in cardiovascular disease. ( 0,801999364986205 )
J Integr Bioinform - Uncovering the expression patterns of chimeric transcripts using surveys of affymetrix GeneChips. ( 0,80054544897402 )
Comput Math Methods Med - Dynamic regulatory network reconstruction for Alzheimer's disease based on matrix decomposition techniques. ( 0,800131326662709 )
Sci Data - Assessment of lipidomic species in hepatocyte lipid droplets from stressed mouse models. ( 0,799802933824067 )
Brief. Bioinformatics - A brief introduction to web-based genome browsers. ( 0,798658640582685 )
Wiley Interdiscip Rev Syst Biol Med - Noncoding RNAs in gene regulation. ( 0,797372259994291 )
Comput. Biol. Med. - Discovering the transcriptional modules using microarray data by penalized matrix decomposition. ( 0,797006733288299 )
Curr Protoc Bioinformatics - BEDTools: The Swiss-Army Tool for Genome Feature Analysis. ( 0,795952493978634 )
J. Comput. Biol. - Markov logic networks in the analysis of genetic data. ( 0,795029631246603 )
Comput Biol Chem - A computational method of predicting regulatory interactions in Arabidopsis based on gene expression data and sequence information. ( 0,792910851241507 )
Wiley Interdiscip Rev Syst Biol Med - Reverse-engineering human regulatory networks. ( 0,792481975606322 )
J Am Med Inform Assoc - Utility of gene-specific algorithms for predicting pathogenicity of uncertain gene variants. ( 0,792415646176777 )
Methods Inf Med - Identification of breast cancer prognosis markers using integrative sparse boosting. ( 0,791268931984277 )
Comput. Biol. Med. - Meta analysis of gene expression changes upon treatment of A549 cells with anti-cancer drugs to identify universal responses. ( 0,789979572678692 )
Wiley Interdiscip Rev Syst Biol Med - Stem cell bioengineering at the interface of systems-based models and high-throughput platforms. ( 0,789062293609149 )
Comput Biol Chem - Revealing weak differential gene expressions and their reproducible functions associated with breast cancer metastasis. ( 0,788999287373929 )
Comput Biol Chem - Exploring the complexity of pathway-drug relationships using latent Dirichlet allocation. ( 0,788766997100012 )
Comput Biol Chem - Gene expression patterns combined with bioinformatics analysis identify genes associated with cholangiocarcinoma. ( 0,788377843438029 )
Brief. Bioinformatics - Evolution of gene regulation--on the road towards computational inferences. ( 0,787001631208378 )
Sci Data - Genomes and phenomes of a population of outbred rats and its progenitors. ( 0,786816442789845 )
Comput. Biol. Med. - Computational gene network study on antibiotic resistance genes of Acinetobacter baumannii. ( 0,786684915898131 )
Wiley Interdiscip Rev Syst Biol Med - Sex and the circuitry: progress toward a systems-level understanding of vertebrate sex determination. ( 0,785953012613058 )
J Biomed Inform - Hemojuvelin-hepcidin axis modeled and analyzed using Petri nets. ( 0,782030372556872 )
J Biomed Inform - CPAS: a trans-omics pathway analysis tool for jointly analyzing DNA copy number variations and mRNA expression profiles data. ( 0,781903318985904 )
Brief. Bioinformatics - Apoptosis regulatory protein-protein interaction demonstrates hierarchical scale-free fractal network. ( 0,780818043823017 )
J Biomed Inform - Structural network analysis of biological networks for assessment of potential disease model organisms. ( 0,780661543085697 )
Comput. Biol. Med. - A review on the computational approaches for gene regulatory network construction. ( 0,780644206940594 )
Comput Biol Chem - Large-scale mining co-expressed genes in Arabidopsis anther: from pair to group. ( 0,780525787613308 )
Curr Protoc Bioinformatics - Using Weeder, Pscan, and PscanChIP for the Discovery of Enriched Transcription Factor Binding Site Motifs in Nucleotide Sequences. ( 0,780516825228126 )
J Biomed Inform - Protein interaction network underpins concordant prognosis among heterogeneous breast cancer signatures. ( 0,780007363094411 )
Comput. Biol. Med. - A molecular prospective provides new insights into implication of PDYN and OPRK1 genes in alcohol dependence. ( 0,778143859795397 )
Comput. Biol. Med. - Network-based approach reveals Y chromosome influences prostate cancer susceptibility. ( 0,777914294767483 )
J Integr Bioinform - Bioinformatics tools help molecular characterization of Perkinsus olseni differentially expressed genes. ( 0,777789395813432 )