Brief. Bioinformatics - Knowledge representation in metabolic pathway databases.

Tópicos

{ gene(2352) biolog(1181) express(1162) }
{ analysi(2126) use(1163) compon(1037) }
{ featur(1941) imag(1645) propos(1176) }
{ howev(809) still(633) remain(590) }
{ research(1085) discuss(1038) issu(1018) }
{ data(1714) softwar(1251) tool(1186) }
{ structur(1116) can(940) graph(676) }
{ measur(2081) correl(1212) valu(896) }
{ sequenc(1873) structur(1644) protein(1328) }
{ concept(1167) ontolog(924) domain(897) }
{ use(2086) technolog(871) perceiv(783) }
{ use(976) code(926) identifi(902) }
{ take(945) account(800) differ(722) }
{ ehr(2073) health(1662) electron(1139) }
{ sampl(1606) size(1419) use(1276) }
{ drug(1928) target(777) effect(648) }
{ result(1111) use(1088) new(759) }
{ process(1125) use(805) approach(778) }
{ can(774) often(719) complex(702) }
{ data(1737) use(1416) pattern(1282) }
{ imag(1057) registr(996) error(939) }
{ framework(1458) process(801) describ(734) }
{ care(1570) inform(1187) nurs(1089) }
{ method(984) reconstruct(947) comput(926) }
{ case(1353) use(1143) diagnosi(1136) }
{ studi(1410) differ(1259) use(1210) }
{ record(1888) medic(1808) patient(1693) }
{ monitor(1329) mobil(1314) devic(1160) }
{ model(2656) set(1616) predict(1553) }
{ time(1939) patient(1703) rate(768) }
{ use(1733) differ(960) four(931) }
{ survey(1388) particip(1329) question(1065) }
{ estim(2440) model(1874) function(577) }
{ decis(3086) make(1611) patient(1517) }
{ model(3404) distribut(989) bayesian(671) }
{ imag(1947) propos(1133) code(1026) }
{ inform(2794) health(2639) internet(1427) }
{ system(1976) rule(880) can(841) }
{ bind(1733) structur(1185) ligand(1036) }
{ 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) }
{ 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) }
{ problem(2511) optim(1539) algorithm(950) }
{ error(1145) method(1030) estim(1020) }
{ chang(1828) time(1643) increas(1301) }
{ 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) }
{ control(1307) perform(991) simul(935) }
{ model(2220) cell(1177) simul(1124) }
{ general(901) number(790) one(736) }
{ search(2224) databas(1162) retriev(909) }
{ data(3963) clinic(1234) research(1004) }
{ risk(3053) factor(974) diseas(938) }
{ perform(999) metric(946) measur(919) }
{ system(1050) medic(1026) inform(1018) }
{ import(1318) role(1303) understand(862) }
{ model(2341) predict(2261) use(1141) }
{ visual(1396) interact(850) tool(830) }
{ compound(1573) activ(1297) structur(1058) }
{ perform(1367) use(1326) method(1137) }
{ studi(1119) effect(1106) posit(819) }
{ blood(1257) pressur(1144) flow(957) }
{ spatial(1525) area(1432) region(1030) }
{ health(3367) inform(1360) care(1135) }
{ model(3480) simul(1196) paramet(876) }
{ state(1844) use(1261) util(961) }
{ research(1218) medic(880) student(794) }
{ patient(2837) hospit(1953) medic(668) }
{ 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) }
{ first(2504) two(1366) second(1323) }
{ intervent(3218) particip(2042) group(1664) }
{ activ(1138) subject(705) human(624) }
{ patient(1821) servic(1111) care(1106) }
{ can(981) present(881) function(850) }
{ health(1844) social(1437) communiti(874) }
{ high(1669) rate(1365) level(1280) }
{ cancer(2502) breast(956) screen(824) }
{ implement(1333) system(1263) develop(1122) }
{ activ(1452) weight(1219) physic(1104) }
{ method(1969) cluster(1462) data(1082) }
{ method(2212) result(1239) propos(1039) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

The accurate representation of all aspects of a metabolic network in a structured format, such that it can be used for a wide variety of computational analyses, is a challenge faced by a growing number of researchers. Analysis of five major metabolic pathway databases reveals that each database has made widely different choices to address this challenge, including how to deal with knowledge that is uncertain or missing. In concise overviews, we show how concepts such as compartments, enzymatic complexes and the direction of reactions are represented in each database. Importantly, also concepts which a database does not represent are described. Which aspects of the metabolic network need to be available in a structured format and to what detail differs per application. For example, for in silico phenotype prediction, a detailed representation of gene-protein-reaction relations and the compartmentalization of the network is essential. Our analysis also shows that current databases are still limited in capturing all details of the biology of the metabolic network, further illustrated with a detailed analysis of three metabolic processes. Finally, we conclude that the conceptual differences between the databases, which make knowledge exchange and integration a challenge, have not been resolved, so far, by the exchange formats in which knowledge representation is standardized.

Resumo Limpo

accur represent aspect metabol network structur format can use wide varieti comput analys challeng face grow number research analysi five major metabol pathway databas reveal databas made wide differ choic address challeng includ deal knowledg uncertain miss concis overview show concept compart enzymat complex direct reaction repres databas import also concept databas repres describ aspect metabol network need avail structur format detail differ per applic exampl silico phenotyp predict detail represent geneproteinreact relat compartment network essenti analysi also show current databas still limit captur detail biolog metabol network illustr detail analysi three metabol process final conclud conceptu differ databas make knowledg exchang integr challeng resolv far exchang format knowledg represent standard

Resumos Similares

Brief. Bioinformatics - Advances in network-based metabolic pathway analysis and gene expression data integration. ( 0,661840119794703 )
Brief. Bioinformatics - Bioinformatics for personal genome interpretation. ( 0,661690741413872 )
Brief. Bioinformatics - Alternative applications for distinct RNA sequencing strategies. ( 0,659763793295154 )
Brief. Bioinformatics - Systems mapping: how to map genes for biomass allocation toward an ideotype. ( 0,655791058497607 )
Brief. Bioinformatics - Lessons from a decade of integrating cancer copy number alterations with gene expression profiles. ( 0,646184585841964 )
Wiley Interdiscip Rev Syst Biol Med - Toward a systems-level understanding of the Hedgehog signaling pathway: defining the complex, robust, and fragile. ( 0,630238365127515 )
Brief. Bioinformatics - Principal component analysis based methods in bioinformatics studies. ( 0,625594820708797 )
J Biomed Inform - CPAS: a trans-omics pathway analysis tool for jointly analyzing DNA copy number variations and mRNA expression profiles data. ( 0,62268581272978 )
Brief. Bioinformatics - Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives. ( 0,621441470280533 )
Brief. Bioinformatics - Toward microRNA-mediated gene regulatory networks in plants. ( 0,620124190932247 )
Wiley Interdiscip Rev Syst Biol Med - Genome network medicine: innovation to overcome huge challenges in cancer therapy. ( 0,615557865538904 )
Brief. Bioinformatics - Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts. ( 0,61097262082247 )
Brief. Bioinformatics - Advantages of mixing bioinformatics and visualization approaches for analyzing sRNA-mediated regulatory bacterial networks. ( 0,61000581457801 )
Brief. Bioinformatics - Learning transcriptional regulation on a genome scale: a theoretical analysis based on gene expression data. ( 0,609977177053888 )
Brief. Bioinformatics - Probabilistic graphical models for genetic association studies. ( 0,606488516655116 )
Brief. Bioinformatics - Computational analysis of miRNA targets in plants: current status and challenges. ( 0,604965925769756 )
Brief. Bioinformatics - Identification of aberrant pathways and network activities from high-throughput data. ( 0,602156966785994 )
Wiley Interdiscip Rev Syst Biol Med - Using variability in gene expression as a tool for studying gene regulation. ( 0,600962310161253 )
Wiley Interdiscip Rev Syst Biol Med - The zebrafish: scalable in vivo modeling for systems biology. ( 0,592682769649953 )
Brief. Bioinformatics - Reconciliation of metabolites and biochemical reactions for metabolic networks. ( 0,591458266910398 )
Brief. Bioinformatics - Introduction into the analysis of high-throughput-sequencing based epigenome data. ( 0,589633132780604 )
Wiley Interdiscip Rev Syst Biol Med - Network biology: a direct approach to study biological function. ( 0,588867585047852 )
J Integr Bioinform - Construction of coffee transcriptome networks based on gene annotation semantics. ( 0,588170660289753 )
Wiley Interdiscip Rev Syst Biol Med - Subdiffractive microscopy: techniques, applications, and challenges. ( 0,587804321528323 )
Wiley Interdiscip Rev Syst Biol Med - Mechanisms of genetic regulation in gene expression: examples from drug metabolizing enzymes and transporters. ( 0,587399429811116 )
Brief. Bioinformatics - Visualizing time-related data in biology, a review. ( 0,587293151839314 )
J. Comput. Biol. - Biological network querying techniques: analysis and comparison. ( 0,587122458545243 )
Wiley Interdiscip Rev Syst Biol Med - Systems vaccinology: learning to compute the behavior of vaccine induced immunity. ( 0,586088045801808 )
Wiley Interdiscip Rev Syst Biol Med - Layers of epistasis: genome-wide regulatory networks and network approaches to genome-wide association studies. ( 0,585728565432415 )
Wiley Interdiscip Rev Syst Biol Med - Quantitative analysis of phosphorylation-based protein signaling networks in the immune system by mass spectrometry. ( 0,585502408593034 )
Brief. Bioinformatics - Combining multidimensional genomic measurements for predicting cancer prognosis: observations from TCGA. ( 0,583633342324936 )
IEEE Trans Image Process - Reciprocal focus profile. ( 0,58343424278155 )
Comput Math Methods Med - A mixture modeling framework for differential analysis of high-throughput data. ( 0,582544372065649 )
Comput Biol Chem - In silico identification of conserved microRNAs and their target transcripts from expressed sequence tags of three earthworm species. ( 0,579453964480784 )
Brief. Bioinformatics - High-performance analysis of biological systems dynamics with the DiVinE model checker. ( 0,572928504375133 )
J Biomed Inform - Independent component analysis: mining microarray data for fundamental human gene expression modules. ( 0,571782405402068 )
AMIA Annu Symp Proc - An ontology-neutral framework for enrichment analysis. ( 0,571657870828634 )
J. Comput. Biol. - Computational disease gene prioritization: an appraisal. ( 0,571181631379919 )
Med Biol Eng Comput - Quantitative calculation of human melatonin suppression induced by inappropriate light at night. ( 0,57091419465319 )
AMIA Annu Symp Proc - Similarity-based disease risk assessment for personal genomes: proof of concept. ( 0,56982500918807 )
Wiley Interdiscip Rev Syst Biol Med - Genome-wide approaches in the study of microRNA biology. ( 0,568826438497572 )
Brief. Bioinformatics - Exon array data analysis using Affymetrix power tools and R statistical software. ( 0,566362474611865 )
Res Synth Methods - Article alerts: items from 2010, part I. ( 0,56543596800223 )
Comput Math Methods Med - First comprehensive in silico analysis of the functional and structural consequences of SNPs in human GalNAc-T1 gene. ( 0,563187461629292 )
Sci Data - Genome-wide functional genomic and transcriptomic analyses for genes regulating sensitivity to vorinostat. ( 0,561329948482465 )
Brief. Bioinformatics - A case-control design for testing and estimating epigenetic effects on complex diseases. ( 0,559926916393978 )
Wiley Interdiscip Rev Syst Biol Med - Pharmacogenomics discovery and implementation in genome-wide association studies era. ( 0,559338873538086 )
J Integr Bioinform - Reconstruction of biological networks based on life science data integration. ( 0,557592098895434 )
Wiley Interdiscip Rev Syst Biol Med - Mechanisms controlling hematopoietic stem cell functions during normal hematopoiesis and hematological malignancies. ( 0,557417434192324 )
J. Comput. Biol. - Comparison of phylogenetic trees and search for a central trend in the forest of life. ( 0,557137640953476 )
Wiley Interdiscip Rev Syst Biol Med - Genomics and epigenomics of colorectal cancer. ( 0,557019558544803 )
J Biomed Inform - Where we stand, where we are moving: Surveying computational techniques for identifying miRNA genes and uncovering their regulatory role. ( 0,556217514128005 )
J Am Med Inform Assoc - An information-gain approach to detecting three-way epistatic interactions in genetic association studies. ( 0,555260845676672 )
Wiley Interdiscip Rev Syst Biol Med - Postgenomic technologies targeting the Wnt signaling network. ( 0,553735655952045 )
Brief. Bioinformatics - An open-pollinated design for mapping imprinting genes in natural populations. ( 0,55324406564077 )
Wiley Interdiscip Rev Syst Biol Med - Signaling networks in palate development. ( 0,553038885496432 )
Comput. Biol. Med. - Nonlinear dimensionality reduction of gene expression data for visualization and clustering analysis of cancer tissue samples. ( 0,552427882178322 )
J Integr Bioinform - Uncovering the expression patterns of chimeric transcripts using surveys of affymetrix GeneChips. ( 0,551480837656768 )
Wiley Interdiscip Rev Syst Biol Med - Bioimage informatics for understanding spatiotemporal dynamics of cellular processes. ( 0,550831998623477 )
Wiley Interdiscip Rev Syst Biol Med - Using a systems biology approach to understand and study the mechanisms of metastasis. ( 0,549765716722808 )
Comput. Biol. Med. - Mathematical modeling and sensitivity analysis of the integrated TNFa-mediated apoptotic pathway for identifying key regulators. ( 0,549415386985817 )
Comput Math Methods Med - Understanding the pathogenesis of Kawasaki disease by network and pathway analysis. ( 0,548330709071059 )
Brief. Bioinformatics - Experimental evidence validating the computational inference of functional associations from gene fusion events: a critical survey. ( 0,547239500605794 )
Wiley Interdiscip Rev Syst Biol Med - Protein microarrays for genome-wide posttranslational modification analysis. ( 0,54709872621471 )
Comput Math Methods Med - Genomic and functional analysis of the toxic effect of tachyplesin I on the embryonic development of zebrafish. ( 0,546761955181621 )
Wiley Interdiscip Rev Syst Biol Med - Cardiac function and disease: emerging role of small ubiquitin-related modifier. ( 0,546434492808556 )
J Chem Inf Model - Using molecular features of xenobiotics to predict hepatic gene expression response. ( 0,545062177082611 )
Wiley Interdiscip Rev Syst Biol Med - Systems biology approaches to epidemiological studies of complex diseases. ( 0,544843561939545 )
Brief. Bioinformatics - Online tools for understanding rat physiology. ( 0,544425216488334 )
Brief. Bioinformatics - Next generation sequencing in functional genomics. ( 0,544422664529105 )
J Chem Inf Model - Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms. ( 0,544408230073924 )
Wiley Interdiscip Rev Syst Biol Med - Whole transcriptome analysis: what are we still missing? ( 0,543386773595589 )
J Biomed Inform - An innovative portal for rare genetic diseases research: the semantic Diseasecard. ( 0,543006983885859 )
Brief. Bioinformatics - The genomic and functional characteristics of disease genes. ( 0,541115048863047 )
Wiley Interdiscip Rev Syst Biol Med - Recent approaches to the prioritization of candidate disease genes. ( 0,540422820419448 )
Brief. Bioinformatics - Evolution and applications of plant pathway resources and databases. ( 0,540402602456972 )
Wiley Interdiscip Rev Syst Biol Med - Recent advances in prostate development and links to prostatic diseases. ( 0,540350079533866 )
Brief. Bioinformatics - Targeted metabolic reconstruction: a novel approach for the characterization of plant-pathogen interactions. ( 0,539265406563942 )
J Biomed Inform - A comparative study of covariance selection models for the inference of gene regulatory networks. ( 0,539007084299372 )
Comput Biol Chem - Using volcano plots and regularized-chi statistics in genetic association studies. ( 0,538871976572765 )
Wiley Interdiscip Rev Syst Biol Med - Potential role of atomic force microscopy in systems biology. ( 0,537406008143263 )
Brief. Bioinformatics - Cancer gene prioritization by integrative analysis of mRNA expression and DNA copy number data: a comparative review. ( 0,536677603025572 )
Comput. Biol. Med. - Revealing pathway maps of renal cell carcinoma by gene expression change. ( 0,536669262351267 )
J Clin Monit Comput - Translational applications of evaluating physiologic variability in human endotoxemia. ( 0,536054574740592 )
Brief. Bioinformatics - Affymetrix GeneChip microarray preprocessing for multivariate analyses. ( 0,535481324800261 )
Curr Protoc Bioinformatics - Using Weeder, Pscan, and PscanChIP for the Discovery of Enriched Transcription Factor Binding Site Motifs in Nucleotide Sequences. ( 0,535186437679069 )
Comput. Biol. Med. - A review on the computational approaches for gene regulatory network construction. ( 0,53514796862246 )
Comput Methods Programs Biomed - Warehousing re-annotated cancer genes for biomarker meta-analysis. ( 0,53476516358283 )
Brief. Bioinformatics - A review of in silico approaches for analysis and prediction of HIV-1-human protein-protein interactions. ( 0,534748684512915 )
Med Biol Eng Comput - Micro/nano-fabrication technologies for cell biology. ( 0,534470165318374 )
Wiley Interdiscip Rev Syst Biol Med - Reverse-engineering human regulatory networks. ( 0,534345811374534 )
J Integr Bioinform - Assembling cell context-specific gene sets: a case in cardiomyopathy. ( 0,534124791929387 )
J. Comput. Biol. - Constructing consensus genetic maps in comparative analysis. ( 0,533376313416152 )
Brief. Bioinformatics - Causes, consequences and solutions of phylogenetic incongruence. ( 0,533324822582435 )
Comput. Biol. Med. - Discovering the transcriptional modules using microarray data by penalized matrix decomposition. ( 0,533210351702814 )
J Am Med Inform Assoc - Utility of gene-specific algorithms for predicting pathogenicity of uncertain gene variants. ( 0,532862215645208 )
Brief. Bioinformatics - Modern bioinformatics meets traditional Chinese medicine. ( 0,532380969713083 )
Brief. Bioinformatics - Combining literature text mining with microarray data: advances for system biology modeling. ( 0,532248251884911 )
Brief. Bioinformatics - From miRNA regulation to miRNA-TF co-regulation: computational approaches and challenges. ( 0,532114712647311 )
J Integr Bioinform - Identification of common carp innate immune genes with whole-genome sequencing and RNA-Seq data. ( 0,531967590245791 )