J Integr Bioinform - Integrated visualization of a multi-omics study of starvation in mouse intestine.

Tópicos

{ result(1111) use(1088) new(759) }
{ gene(2352) biolog(1181) express(1162) }
{ studi(1119) effect(1106) posit(819) }
{ high(1669) rate(1365) level(1280) }
{ visual(1396) interact(850) tool(830) }
{ data(3008) multipl(1320) sourc(1022) }
{ data(1714) softwar(1251) tool(1186) }
{ control(1307) perform(991) simul(935) }
{ perform(999) metric(946) measur(919) }
{ research(1085) discuss(1038) issu(1018) }
{ sequenc(1873) structur(1644) protein(1328) }
{ patient(2315) diseas(1263) diabet(1191) }
{ framework(1458) process(801) describ(734) }
{ chang(1828) time(1643) increas(1301) }
{ can(774) often(719) complex(702) }
{ system(1976) rule(880) can(841) }
{ imag(1057) registr(996) error(939) }
{ method(1219) similar(1157) match(930) }
{ assess(1506) score(1403) qualiti(1306) }
{ treatment(1704) effect(941) patient(846) }
{ concept(1167) ontolog(924) domain(897) }
{ method(984) reconstruct(947) comput(926) }
{ import(1318) role(1303) understand(862) }
{ record(1888) medic(1808) patient(1693) }
{ first(2504) two(1366) second(1323) }
{ activ(1138) subject(705) human(624) }
{ use(2086) technolog(871) perceiv(783) }
{ structur(1116) can(940) graph(676) }
{ implement(1333) system(1263) develop(1122) }
{ decis(3086) make(1611) patient(1517) }
{ detect(2391) sensit(1101) algorithm(908) }
{ model(3404) distribut(989) bayesian(671) }
{ imag(1947) propos(1133) code(1026) }
{ data(1737) use(1416) pattern(1282) }
{ inform(2794) health(2639) internet(1427) }
{ measur(2081) correl(1212) valu(896) }
{ bind(1733) structur(1185) ligand(1036) }
{ featur(3375) classif(2383) classifi(1994) }
{ imag(2830) propos(1344) filter(1198) }
{ network(2748) neural(1063) input(814) }
{ imag(2675) segment(2577) method(1081) }
{ take(945) account(800) differ(722) }
{ studi(2440) review(1878) systemat(933) }
{ motion(1329) object(1292) video(1091) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ problem(2511) optim(1539) algorithm(950) }
{ error(1145) method(1030) estim(1020) }
{ learn(2355) train(1041) set(1003) }
{ clinic(1479) use(1117) guidelin(835) }
{ algorithm(1844) comput(1787) effici(935) }
{ extract(1171) text(1153) clinic(932) }
{ method(1557) propos(1049) approach(1037) }
{ 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) }
{ 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) }
{ system(1050) medic(1026) inform(1018) }
{ model(2341) predict(2261) use(1141) }
{ compound(1573) activ(1297) structur(1058) }
{ perform(1367) use(1326) method(1137) }
{ blood(1257) pressur(1144) flow(957) }
{ spatial(1525) area(1432) region(1030) }
{ 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) }
{ 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) }
{ sampl(1606) size(1419) use(1276) }
{ intervent(3218) particip(2042) group(1664) }
{ time(1939) patient(1703) rate(768) }
{ patient(1821) servic(1111) care(1106) }
{ can(981) present(881) function(850) }
{ analysi(2126) use(1163) compon(1037) }
{ health(1844) social(1437) communiti(874) }
{ cancer(2502) breast(956) screen(824) }
{ use(976) code(926) identifi(902) }
{ use(1733) differ(960) four(931) }
{ drug(1928) target(777) effect(648) }
{ survey(1388) particip(1329) question(1065) }
{ estim(2440) model(1874) function(577) }
{ process(1125) use(805) approach(778) }
{ activ(1452) weight(1219) physic(1104) }
{ method(1969) cluster(1462) data(1082) }
{ method(2212) result(1239) propos(1039) }

Resumo

Our understanding of complex biological processes can be enhanced by combining different kinds of high-throughput experimental data, but the use of incompatible identifiers makes data integration a challenge. We aimed to improve methods for integrating and visualizing different types of omics data. To validate these methods, we applied them to two previous studies on starvation in mice, one using proteomics and the other using transcriptomics technology. We extended the PathVisio software with new plugins to link proteins, transcripts and pathways. A low overall correlation between proteome and transcriptome data was detected (Spearman rank correlation: 0.21). At the level of individual genes, correlation was highly variable. Many mRNA/protein pairs, such as fructose biphosphate aldolase B and ATP Synthase, show good correlation. For other pairs, such as ferritin and elongation factor 2, an interesting effect is observed, where mRNA and protein levels change in opposite directions, suggesting they are not primarily regulated at the transcriptional level. We used pathway diagrams to visualize the integrated datasets and found it encouraging that transcriptomics and proteomics data supported each other at the pathway level. Visualization of the integrated dataset on pathways led to new observations on gene-regulation in the response of the gut to starvation. Our methods are generic and can be applied to any multi-omics study. The PathVisio software can be obtained at http://www.pathvisio.org. Supplemental data are available at http://www.bigcat.unimaas.nl/data/jib-supplemental/ , including instructions on reproducing the pathway visualizations of this manuscript.

Resumo Limpo

understand complex biolog process can enhanc combin differ kind highthroughput experiment data use incompat identifi make data integr challeng aim improv method integr visual differ type omic data valid method appli two previous studi starvat mice one use proteom use transcriptom technolog extend pathvisio softwar new plugin link protein transcript pathway low overal correl proteom transcriptom data detect spearman rank correl level individu gene correl high variabl mani mrnaprotein pair fructos biphosph aldolas b atp synthas show good correl pair ferritin elong factor interest effect observ mrna protein level chang opposit direct suggest primarili regul transcript level use pathway diagram visual integr dataset found encourag transcriptom proteom data support pathway level visual integr dataset pathway led new observ generegul respons gut starvat method generic can appli multiom studi pathvisio softwar can obtain httpwwwpathvisioorg supplement data avail httpwwwbigcatunimaasnldatajibsupplement includ instruct reproduc pathway visual manuscript

Resumos Similares

J Med Syst - Computer anxiety in nursing: an investigation from Turkish nurses. ( 0,679667298496207 )
Lifetime Data Anal - Copula identifiability conditions for dependent truncated data model. ( 0,641910002310734 )
Comput Biol Chem - Hierarchical closeness efficiently predicts disease genes in a directed signaling network. ( 0,620136693985309 )
Comput Biol Chem - lncRNAMap: a map of putative regulatory functions in the long non-coding transcriptome. ( 0,612914674479118 )
Comput. Biol. Med. - Promoter recognition based on the maximum entropy hidden Markov model. ( 0,607558552316166 )
Wiley Interdiscip Rev Syst Biol Med - Using a systems biology approach to understand and study the mechanisms of metastasis. ( 0,599975908153671 )
J Biomed Inform - A comparative study of covariance selection models for the inference of gene regulatory networks. ( 0,599739352955951 )
Brief. Bioinformatics - OrthoDisease: tracking disease gene orthologs across 100 species. ( 0,596173603484357 )
Brief. Bioinformatics - Kernel methods for large-scale genomic data analysis. ( 0,591015921193433 )
Comput. Biol. Med. - A molecular prospective provides new insights into implication of PDYN and OPRK1 genes in alcohol dependence. ( 0,589444159526598 )
J Integr Bioinform - Integration of -omics data and networks for biomedical research with VANTED. ( 0,588980794578532 )
J Biomed Inform - Gene pathways and subnetworks distinguish between major glioma subtypes and elucidate potential underlying biology. ( 0,582570230978545 )
Brief. Bioinformatics - From miRNA regulation to miRNA-TF co-regulation: computational approaches and challenges. ( 0,582408334396549 )
Comput Biol Chem - Statistical analysis of combinatorial transcriptional regulatory motifs in human intron-containing promoter sequences. ( 0,570813398602191 )
Wiley Interdiscip Rev Syst Biol Med - Engineered genetic information processing circuits. ( 0,570717206643688 )
Comput Biol Chem - Using volcano plots and regularized-chi statistics in genetic association studies. ( 0,568837830523033 )
J Biomed Inform - Systems-based biological concordance and predictive reproducibility of gene set discovery methods in cardiovascular disease. ( 0,567074362201111 )
Comput Biol Chem - In silico identification of conserved microRNAs and their target transcripts from expressed sequence tags of three earthworm species. ( 0,565885401462017 )
J. Comput. Biol. - Inferring mechanisms of compensation from E-MAP and SGA data using local search algorithms for max cut. ( 0,565285572412877 )
AMIA Annu Symp Proc - Towards mechanism classifiers: expression-anchored Gene Ontology signature predicts clinical outcome in lung adenocarcinoma patients. ( 0,564709454796069 )
Brief. Bioinformatics - Towards a bioinformatics analysis of anti-Alzheimer's herbal medicines from a target network perspective. ( 0,557132624188633 )
J Integr Bioinform - Towards prediction and prioritization of disease genes by the modularity of human phenome-genome assembled network. ( 0,556506517780944 )
Artif Intell Med - Identifying regulatory relationships among genomic loci, biological pathways, and disease. ( 0,552321155904884 )
IEEE Trans Image Process - Discriminative shared Gaussian processes for multiview and view-invariant facial expression recognition. ( 0,552094379357259 )
Methods Inf Med - Pathway based microarray analysis, utilising enzyme compounds and cascade events. ( 0,551687598871043 )
Comput. Biol. Med. - Computational identification of operon-like transcriptional loci in eukaryotes. ( 0,551362033091938 )
Comput Biol Chem - Neighbor-favoring weight reinforcement to improve random walk-based disease gene prioritization. ( 0,551018183957721 )
Comput Biol Chem - Bioinformatic analysis of molecular network of glucosinolate biosynthesis. ( 0,550675123984347 )
J Biomed Inform - A two step method to identify clinical outcome relevant genes with microarray data. ( 0,550431215691042 )
Comput Math Methods Med - Molecular signature of cancer at gene level or pathway level? Case studies of colorectal cancer and prostate cancer microarray data. ( 0,549779662498987 )
Brief. Bioinformatics - Mathematical modeling of biological systems. ( 0,549256031170283 )
Comput. Biol. Med. - Extracting plants core genes responding to abiotic stresses by penalized matrix decomposition. ( 0,546383288906829 )
Brief. Bioinformatics - Learning transcriptional regulation on a genome scale: a theoretical analysis based on gene expression data. ( 0,543138007779188 )
J Biomed Inform - Structural network analysis of biological networks for assessment of potential disease model organisms. ( 0,542635288944852 )
Comput Biol Chem - Identifying novel prostate cancer associated pathways based on integrative microarray data analysis. ( 0,541830995087943 )
Wiley Interdiscip Rev Syst Biol Med - Mechanisms of genetic regulation in gene expression: examples from drug metabolizing enzymes and transporters. ( 0,541606141661523 )
Comput Biol Chem - Disruption of murine Tcte3-3 induces tissue specific apoptosis via co-expression of Anxa5 and Pebp1. ( 0,537642930463572 )
Wiley Interdiscip Rev Syst Biol Med - Reverse-engineering human regulatory networks. ( 0,537077882561308 )
J Am Med Inform Assoc - Complex-disease networks of trait-associated single-nucleotide polymorphisms (SNPs) unveiled by information theory. ( 0,536418155128293 )
Brief. Bioinformatics - Predictive modelling of gene expression from transcriptional regulatory elements. ( 0,536404960295265 )
Methods Inf Med - Affective medicine. A review of affective computing efforts in medical informatics. ( 0,534234380221029 )
Brief. Bioinformatics - Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. ( 0,533661204559844 )
Sci Data - Genome-wide functional genomic and transcriptomic analyses for genes regulating sensitivity to vorinostat. ( 0,532577235793516 )
J Am Med Inform Assoc - Knowledge boosting: a graph-based integration approach with multi-omics data and genomic knowledge for cancer clinical outcome prediction. ( 0,532519584438255 )
J Biomed Inform - Autism candidate genes via mouse phenomics. ( 0,530974897678687 )
Wiley Interdiscip Rev Syst Biol Med - Using variability in gene expression as a tool for studying gene regulation. ( 0,530790995816715 )
Brief. Bioinformatics - Revealing the architecture of genetic and epigenetic regulation: a maximum likelihood model. ( 0,529486955159024 )
Wiley Interdiscip Rev Syst Biol Med - Where gene discovery turns into systems biology: genome-scale RNAi screens in Drosophila. ( 0,529298391127636 )
Wiley Interdiscip Rev Syst Biol Med - The zebrafish: scalable in vivo modeling for systems biology. ( 0,528535285388651 )
Comput Math Methods Med - First comprehensive in silico analysis of the functional and structural consequences of SNPs in human GalNAc-T1 gene. ( 0,525455222418754 )
J Am Med Inform Assoc - An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer. ( 0,52520776044705 )
J Integr Bioinform - Predicting breast cancer chemotherapeutic response using a novel tool for microarray data analysis. ( 0,523919975360506 )
Sci Data - DNA methylation temporal profiling following peripheral versus central nervous system axotomy. ( 0,523190639585253 )
J Am Med Inform Assoc - Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseases. ( 0,522461388677905 )
Brief. Bioinformatics - Probe mapping across multiple microarray platforms. ( 0,522440623471966 )
J Biomed Inform - Analysis of functional and pathway association of differential co-expressed genes: a case study in drug addiction. ( 0,522011335226349 )
Comput. Biol. Med. - Degrees of separation as a statistical tool for evaluating candidate genes. ( 0,521655429745329 )
Comput. Biol. Med. - Identification and analysis of the regulatory network of Myc and microRNAs from high-throughput experimental data. ( 0,521272871291683 )
Artif Intell Med - Phased searching with NEAT in a time-scaled framework: experiments on a computer-aided detection system for lung nodules. ( 0,521148775206619 )
Comput. Biol. Med. - Contractions of the whole and longitudinally cut rat's portal vein. ( 0,520306734151123 )
J Biomed Inform - Prioritization of potential candidate disease genes by topological similarity of protein-protein interaction network and phenotype data. ( 0,520287994253928 )
Wiley Interdiscip Rev Syst Biol Med - Network biology: a direct approach to study biological function. ( 0,518512073614587 )
Wiley Interdiscip Rev Syst Biol Med - Recent advances in prostate development and links to prostatic diseases. ( 0,517901564105645 )
J Biomed Inform - Hemojuvelin-hepcidin axis modeled and analyzed using Petri nets. ( 0,517823155607182 )
J. Comput. Biol. - Optimally orienting physical networks. ( 0,51739268678517 )
Sci Data - Genomes and phenomes of a population of outbred rats and its progenitors. ( 0,516469760407609 )
Brief. Bioinformatics - Exploring the function of genetic variants in the non-coding genomic regions: approaches for identifying human regulatory variants affecting gene expression. ( 0,515546356624483 )
Brief. Bioinformatics - Identification of aberrant pathways and network activities from high-throughput data. ( 0,515002645310251 )
Comput Biol Chem - Expression patterns of photoperiod and temperature regulated heading date genes in Oryza sativa. ( 0,51366511246781 )
J Biomed Inform - Independent component analysis: mining microarray data for fundamental human gene expression modules. ( 0,513170646324161 )
Brief. Bioinformatics - Introduction into the analysis of high-throughput-sequencing based epigenome data. ( 0,51234053780798 )
Comput Math Methods Med - Dynamic regulatory network reconstruction for Alzheimer's disease based on matrix decomposition techniques. ( 0,512021281570103 )
Comput Methods Programs Biomed - Ensemble transcript interaction networks: a case study on Alzheimer's disease. ( 0,511397744215753 )
Comput Methods Programs Biomed - Warehousing re-annotated cancer genes for biomarker meta-analysis. ( 0,511330059608708 )
IEEE J Biomed Health Inform - Integrative clustering by nonnegative matrix factorization can reveal coherent functional groups from gene profile data. ( 0,511047203570122 )
Curr Protoc Bioinformatics - BEDTools: The Swiss-Army Tool for Genome Feature Analysis. ( 0,510941703603495 )
Wiley Interdiscip Rev Syst Biol Med - Decoding the functions of post-transcriptional regulators in the determination of inflammatory states: focus on macrophage activation. ( 0,510015455491447 )
Comput Biol Chem - Global expression analysis of miRNA gene cluster and family based on isomiRs from deep sequencing data. ( 0,509754065859016 )
Comput Math Methods Med - Integrating gene expression and protein interaction data for signaling pathway prediction of Alzheimer's disease. ( 0,509237487509967 )
J Integr Bioinform - SNPRanker: a tool for identification and scoring of SNPs associated to target genes. ( 0,509126426259088 )
J Integr Bioinform - An integrative bioinformatics framework for genome-scale multiple level network reconstruction of rice. ( 0,508738690787417 )
Wiley Interdiscip Rev Syst Biol Med - Genome network medicine: innovation to overcome huge challenges in cancer therapy. ( 0,508623433856348 )
Wiley Interdiscip Rev Syst Biol Med - Noncoding RNAs in gene regulation. ( 0,508598169245303 )
Wiley Interdiscip Rev Syst Biol Med - Cardiac function and disease: emerging role of small ubiquitin-related modifier. ( 0,508565648488293 )
Wiley Interdiscip Rev Syst Biol Med - Postgenomic technologies targeting the Wnt signaling network. ( 0,508063801268601 )
Comput Biol Chem - Prediction and verification of microRNAs related to proline accumulation under drought stress in potato. ( 0,507455363083688 )
Artif Intell Med - Interactive web service system for exploration of biological pathways. ( 0,5072351743993 )
J. Comput. Biol. - Vavien: an algorithm for prioritizing candidate disease genes based on topological similarity of proteins in interaction networks. ( 0,507008954478462 )
J Integr Bioinform - Network expansion and pathway enrichment analysis towards biologically significant findings from microarrays. ( 0,505395228904652 )
J. Comput. Biol. - Experiment specific expression patterns. ( 0,505255113365429 )
J. Comput. Biol. - A topology-based score for pathway enrichment. ( 0,505159983204153 )
Perspect Health Inf Manag - Flexible approaches for teaching computational genomics in a health information management program. ( 0,504455174194595 )
J Biomed Inform - Relational machine learning for electronic health record-driven phenotyping. ( 0,504303295555458 )
Brief. Bioinformatics - Dissection of human MiRNA regulatory influence to subpathway. ( 0,503959097245994 )
J. Comput. Biol. - Markov logic networks in the analysis of genetic data. ( 0,503840873444539 )
J Am Med Inform Assoc - Extracting coordinated patterns of DNA methylation and gene expression in ovarian cancer. ( 0,503125801624557 )
J Integr Bioinform - Assembling cell context-specific gene sets: a case in cardiomyopathy. ( 0,503055679955583 )
J Am Med Inform Assoc - Identifying disease genes and module biomarkers by differential interactions. ( 0,501906505334921 )
AMIA Annu Symp Proc - Similarity-based disease risk assessment for personal genomes: proof of concept. ( 0,501643835096203 )
Wiley Interdiscip Rev Syst Biol Med - Sex and the circuitry: progress toward a systems-level understanding of vertebrate sex determination. ( 0,500921657308848 )