Comput Biol Chem - Bioinformatic analysis of molecular network of glucosinolate biosynthesis.

Tópicos

{ gene(2352) biolog(1181) express(1162) }
{ data(1737) use(1416) pattern(1282) }
{ data(1714) softwar(1251) tool(1186) }
{ model(2656) set(1616) predict(1553) }
{ visual(1396) interact(850) tool(830) }
{ error(1145) method(1030) estim(1020) }
{ method(1557) propos(1049) approach(1037) }
{ import(1318) role(1303) understand(862) }
{ high(1669) rate(1365) level(1280) }
{ process(1125) use(805) approach(778) }
{ system(1976) rule(880) can(841) }
{ network(2748) neural(1063) input(814) }
{ chang(1828) time(1643) increas(1301) }
{ studi(1119) effect(1106) posit(819) }
{ monitor(1329) mobil(1314) devic(1160) }
{ group(2977) signific(1463) compar(1072) }
{ use(976) code(926) identifi(902) }
{ model(3404) distribut(989) bayesian(671) }
{ can(774) often(719) complex(702) }
{ bind(1733) structur(1185) ligand(1036) }
{ treatment(1704) effect(941) patient(846) }
{ model(2220) cell(1177) simul(1124) }
{ howev(809) still(633) remain(590) }
{ perform(999) metric(946) measur(919) }
{ research(1085) discuss(1038) issu(1018) }
{ compound(1573) activ(1297) structur(1058) }
{ ehr(2073) health(1662) electron(1139) }
{ data(3008) multipl(1320) sourc(1022) }
{ time(1939) patient(1703) rate(768) }
{ use(2086) technolog(871) perceiv(783) }
{ can(981) present(881) function(850) }
{ structur(1116) can(940) graph(676) }
{ use(1733) differ(960) four(931) }
{ imag(1947) propos(1133) code(1026) }
{ inform(2794) health(2639) internet(1427) }
{ measur(2081) correl(1212) valu(896) }
{ imag(1057) registr(996) error(939) }
{ 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) }
{ assess(1506) score(1403) qualiti(1306) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ framework(1458) process(801) describ(734) }
{ problem(2511) optim(1539) algorithm(950) }
{ learn(2355) train(1041) set(1003) }
{ concept(1167) ontolog(924) domain(897) }
{ clinic(1479) use(1117) guidelin(835) }
{ algorithm(1844) comput(1787) effici(935) }
{ extract(1171) text(1153) clinic(932) }
{ design(1359) user(1324) use(1319) }
{ control(1307) perform(991) simul(935) }
{ 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) }
{ 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) }
{ perform(1367) use(1326) method(1137) }
{ 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) }
{ 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) }
{ sampl(1606) size(1419) use(1276) }
{ first(2504) two(1366) second(1323) }
{ intervent(3218) particip(2042) group(1664) }
{ activ(1138) subject(705) human(624) }
{ patient(1821) servic(1111) care(1106) }
{ analysi(2126) use(1163) compon(1037) }
{ health(1844) social(1437) communiti(874) }
{ cancer(2502) breast(956) screen(824) }
{ drug(1928) target(777) effect(648) }
{ result(1111) use(1088) new(759) }
{ implement(1333) system(1263) develop(1122) }
{ survey(1388) particip(1329) question(1065) }
{ estim(2440) model(1874) function(577) }
{ decis(3086) make(1611) patient(1517) }
{ 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

Glucosinolates constitute a major group of secondary metabolites in Arabidopsis, which play an important role in plant interaction with pathogens and insects. Advances in glucosinolate research have defined the biosynthetic pathways. However, cross-talk and interaction between glucosinolate pathway and other molecular pathways are largely unknown. Here three bioinformatics tools were used to explore novel components and pathway connections in glucosinolate network. Although none of the software tools were prefect to predict glucosinolate genes, combination of results generated by all the tools led to successful prediction of all known glucosinolate genes. This approach was used to predict new genes in glucosinolate network. A total of 330 genes were found with high potential to relate to glucosinolate biosynthesis. Among them 64 genes were selected to construct glucosinolate network because their individual connection to at least one known glucosinolate gene was predicted by all the software tools. Microarray data of candidate gene mutants were used for validation of the results. The mutants of nine genes predicted by glucosinolate seed genes all exhibited changes in the expression of glucosinolate genes. Four of the genes have been well-known to functionally interact with glucosinolate biosynthesis. These results indicate that the approach we took provides a powerful way to reveal new players in glucosinolate networks. Creation of an in silico network of glucosinolate biosynthesis will allow the generation of many testable hypotheses and ultimately enable predictive biology.

Resumo Limpo

glucosinol constitut major group secondari metabolit arabidopsi play import role plant interact pathogen insect advanc glucosinol research defin biosynthet pathway howev crosstalk interact glucosinol pathway molecular pathway larg unknown three bioinformat tool use explor novel compon pathway connect glucosinol network although none softwar tool prefect predict glucosinol gene combin result generat tool led success predict known glucosinol gene approach use predict new gene glucosinol network total gene found high potenti relat glucosinol biosynthesi among gene select construct glucosinol network individu connect least one known glucosinol gene predict softwar tool microarray data candid gene mutant use valid result mutant nine gene predict glucosinol seed gene exhibit chang express glucosinol gene four gene wellknown function interact glucosinol biosynthesi result indic approach took provid power way reveal new player glucosinol network creation silico network glucosinol biosynthesi will allow generat mani testabl hypothes ultim enabl predict biolog

Resumos Similares

Brief. Bioinformatics - Revealing the architecture of genetic and epigenetic regulation: a maximum likelihood model. ( 0,888686703408001 )
J Am Med Inform Assoc - Identifying disease genes and module biomarkers by differential interactions. ( 0,881676696993737 )
Comput. Biol. Med. - Identification and analysis of the regulatory network of Myc and microRNAs from high-throughput experimental data. ( 0,880494443116363 )
J. Comput. Biol. - An algorithm for efficient identification of branched metabolic pathways. ( 0,873922044948714 )
Wiley Interdiscip Rev Syst Biol Med - Diverse functional networks of Tbx3 in development and disease. ( 0,872688605640105 )
J Am Med Inform Assoc - Extracting coordinated patterns of DNA methylation and gene expression in ovarian cancer. ( 0,866080776935932 )
J. Comput. Biol. - A topology-based score for pathway enrichment. ( 0,865211235695529 )
Comput Math Methods Med - First comprehensive in silico analysis of the functional and structural consequences of SNPs in human GalNAc-T1 gene. ( 0,859519438357494 )
J Integr Bioinform - Towards prediction and prioritization of disease genes by the modularity of human phenome-genome assembled network. ( 0,858584779259357 )
J. Comput. Biol. - Bioinformatics method to analyze the mechanism of pancreatic cancer disorder. ( 0,858543237232919 )
Comput Biol Chem - Disruption of murine Tcte3-3 induces tissue specific apoptosis via co-expression of Anxa5 and Pebp1. ( 0,856557216480025 )
Comput Math Methods Med - Integrating gene expression and protein interaction data for signaling pathway prediction of Alzheimer's disease. ( 0,855066827136895 )
Wiley Interdiscip Rev Syst Biol Med - Recent advances in prostate development and links to prostatic diseases. ( 0,853973893251166 )
J Integr Bioinform - Network expansion and pathway enrichment analysis towards biologically significant findings from microarrays. ( 0,852640752497612 )
J Am Med Inform Assoc - Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseases. ( 0,851471931472914 )
J Integr Bioinform - An integrative bioinformatics framework for genome-scale multiple level network reconstruction of rice. ( 0,850662997589623 )
Brief. Bioinformatics - Identifying miRNAs, targets and functions. ( 0,850662332376958 )
Sci Data - DNA methylation temporal profiling following peripheral versus central nervous system axotomy. ( 0,848877325839748 )
Wiley Interdiscip Rev Syst Biol Med - Signaling networks in palate development. ( 0,84761370157739 )
Comput. Biol. Med. - Degrees of separation as a statistical tool for evaluating candidate genes. ( 0,846872210140317 )
Comput Biol Chem - Using volcano plots and regularized-chi statistics in genetic association studies. ( 0,846358993970181 )
Comput Biol Chem - Identifying novel prostate cancer associated pathways based on integrative microarray data analysis. ( 0,84443843740424 )
AMIA Annu Symp Proc - Mining disease fingerprints from within genetic pathways. ( 0,843569715506588 )
Wiley Interdiscip Rev Syst Biol Med - Systems biology of adipose tissue metabolism: regulation of growth, signaling and inflammation. ( 0,842306701915985 )
J Am Med Inform Assoc - An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer. ( 0,842082719215786 )
Artif Intell Med - Identifying regulatory relationships among genomic loci, biological pathways, and disease. ( 0,839653363830382 )
Comput. Biol. Med. - Mathematical modeling and sensitivity analysis of the integrated TNFa-mediated apoptotic pathway for identifying key regulators. ( 0,839611020065707 )
Wiley Interdiscip Rev Syst Biol Med - Postgenomic technologies targeting the Wnt signaling network. ( 0,839436824524552 )
J Biomed Inform - A comparative study of covariance selection models for the inference of gene regulatory networks. ( 0,839009294271516 )
Comput Biol Chem - Deciphering histone code of transcriptional regulation in malaria parasites by large-scale data mining. ( 0,836961056205583 )
Wiley Interdiscip Rev Syst Biol Med - miRNA regulation in the context of functional protein networks: principles and applications. ( 0,836651642621029 )
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. ( 0,836477790860166 )
J Am Med Inform Assoc - Knowledge boosting: a graph-based integration approach with multi-omics data and genomic knowledge for cancer clinical outcome prediction. ( 0,835811566204363 )
Wiley Interdiscip Rev Syst Biol Med - Mediators and dynamics of DNA methylation. ( 0,833652388755002 )
J Biomed Inform - Gene pathways and subnetworks distinguish between major glioma subtypes and elucidate potential underlying biology. ( 0,829936398201183 )
Comput Biol Chem - Expression patterns of photoperiod and temperature regulated heading date genes in Oryza sativa. ( 0,829536181031633 )
J. Comput. Biol. - Vavien: an algorithm for prioritizing candidate disease genes based on topological similarity of proteins in interaction networks. ( 0,828063029081747 )
Comput Math Methods Med - Understanding the pathogenesis of Kawasaki disease by network and pathway analysis. ( 0,826891473659421 )
J Integr Bioinform - Knowledge enrichment analysis for human tissue-specific genes uncover new biological insights. ( 0,825182958166126 )
Brief. Bioinformatics - Targeted metabolic reconstruction: a novel approach for the characterization of plant-pathogen interactions. ( 0,824888002995752 )
J Integr Bioinform - Assembling cell context-specific gene sets: a case in cardiomyopathy. ( 0,824653917883216 )
Wiley Interdiscip Rev Syst Biol Med - Using variability in gene expression as a tool for studying gene regulation. ( 0,821735231255035 )
J Chem Inf Model - Using molecular features of xenobiotics to predict hepatic gene expression response. ( 0,819692308546458 )
Comput Math Methods Med - Dynamic regulatory network reconstruction for Alzheimer's disease based on matrix decomposition techniques. ( 0,819524333512503 )
Sci Data - Transcriptomic analysis of midbrain and individual hindbrain rhombomeres in the chick embryo. ( 0,815755587428741 )
Wiley Interdiscip Rev Syst Biol Med - The zebrafish: scalable in vivo modeling for systems biology. ( 0,814296144929714 )
Wiley Interdiscip Rev Syst Biol Med - Where gene discovery turns into systems biology: genome-scale RNAi screens in Drosophila. ( 0,814248416668338 )
J Biomed Inform - The detection of risk pathways, regulated by miRNAs, via the integration of sample-matched miRNA-mRNA profiles and pathway structure. ( 0,813544011911566 )
J Am Med Inform Assoc - Complex-disease networks of trait-associated single-nucleotide polymorphisms (SNPs) unveiled by information theory. ( 0,812713186450984 )
Wiley Interdiscip Rev Syst Biol Med - Regulatory variation: an emerging vantage point for cancer biology. ( 0,812366753711826 )
J. Comput. Biol. - Computational disease gene prioritization: an appraisal. ( 0,812295082119226 )
Brief. Bioinformatics - Identification of aberrant pathways and network activities from high-throughput data. ( 0,812225191040556 )
Wiley Interdiscip Rev Syst Biol Med - Using a systems biology approach to understand and study the mechanisms of metastasis. ( 0,811352592866026 )
J Biomed Inform - Autism candidate genes via mouse phenomics. ( 0,811256256685776 )
Curr Protoc Bioinformatics - BEDTools: The Swiss-Army Tool for Genome Feature Analysis. ( 0,810957375137382 )
Comput. Biol. Med. - Revealing pathway maps of renal cell carcinoma by gene expression change. ( 0,810508609121697 )
Comput Biol Chem - Large-scale mining co-expressed genes in Arabidopsis anther: from pair to group. ( 0,810318680990391 )
Artif Intell Med - An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods. ( 0,81025668184614 )
Wiley Interdiscip Rev Syst Biol Med - Reverse-engineering human regulatory networks. ( 0,810143328322107 )
Comput. Biol. Med. - A review on the computational approaches for gene regulatory network construction. ( 0,810093344888667 )
Brief. Bioinformatics - Apoptosis regulatory protein-protein interaction demonstrates hierarchical scale-free fractal network. ( 0,809215698798697 )
Wiley Interdiscip Rev Syst Biol Med - Network biology: a direct approach to study biological function. ( 0,808871313604372 )
Wiley Interdiscip Rev Syst Biol Med - Integrating omics into the cardiac differentiation of human pluripotent stem cells. ( 0,808236798404928 )
J Integr Bioinform - A study of the short and long-term regulation of E. coli metabolic pathways. ( 0,80810018687133 )
Comput Biol Chem - Exploring the complexity of pathway-drug relationships using latent Dirichlet allocation. ( 0,807887695626807 )
Comput. Biol. Med. - A molecular prospective provides new insights into implication of PDYN and OPRK1 genes in alcohol dependence. ( 0,805780729198191 )
Wiley Interdiscip Rev Syst Biol Med - Cardiac function and disease: emerging role of small ubiquitin-related modifier. ( 0,805300978626041 )
J Biomed Inform - Prioritization of potential candidate disease genes by topological similarity of protein-protein interaction network and phenotype data. ( 0,804385595148089 )
Wiley Interdiscip Rev Syst Biol Med - Sex and the circuitry: progress toward a systems-level understanding of vertebrate sex determination. ( 0,803039875563276 )
Methods Inf Med - Pathway based microarray analysis, utilising enzyme compounds and cascade events. ( 0,802483051303463 )
J Integr Bioinform - Uncovering the expression patterns of chimeric transcripts using surveys of affymetrix GeneChips. ( 0,802301752930176 )
Comput Biol Chem - Using gene expression programming to infer gene regulatory networks from time-series data. ( 0,800846932906478 )
Comput Biol Chem - Gene expression patterns combined with bioinformatics analysis identify genes associated with cholangiocarcinoma. ( 0,800526035021086 )
J Am Med Inform Assoc - Using systems and structure biology tools to dissect cellular phenotypes. ( 0,799767139963168 )
J Biomed Inform - Where we stand, where we are moving: Surveying computational techniques for identifying miRNA genes and uncovering their regulatory role. ( 0,798101943725857 )
Wiley Interdiscip Rev Syst Biol Med - Noncoding RNAs in gene regulation. ( 0,797695942551127 )
J Biomed Inform - Comparative analysis of a novel disease phenotype network based on clinical manifestations. ( 0,79714667156522 )
Brief. Bioinformatics - Toward microRNA-mediated gene regulatory networks in plants. ( 0,795883291511919 )
Comput. Biol. Med. - Computational gene network study on antibiotic resistance genes of Acinetobacter baumannii. ( 0,795771993809184 )
Curr Protoc Bioinformatics - Using Weeder, Pscan, and PscanChIP for the Discovery of Enriched Transcription Factor Binding Site Motifs in Nucleotide Sequences. ( 0,795495093127855 )
IEEE J Biomed Health Inform - Using evolutional properties of gene networks in understanding survival prognosis of glioblastoma. ( 0,795335074435594 )
Wiley Interdiscip Rev Syst Biol Med - Engineered genetic information processing circuits. ( 0,794899330075215 )
Wiley Interdiscip Rev Syst Biol Med - Cyclic nucleotide signaling in intestinal epithelia: getting to the gut of the matter. ( 0,79429676264839 )
J Biomed Inform - Inferring cell cycle feedback regulation from gene expression data. ( 0,793938522687908 )
J Biomed Inform - Independent component analysis: mining microarray data for fundamental human gene expression modules. ( 0,793938522687908 )
J Am Med Inform Assoc - Advantages of genomic complexity: bioinformatics opportunities in microRNA cancer signatures. ( 0,793567496141023 )
Brief. Bioinformatics - Evolution of gene regulation--on the road towards computational inferences. ( 0,793188560377835 )
J Integr Bioinform - Bioinformatics tools help molecular characterization of Perkinsus olseni differentially expressed genes. ( 0,792041864191875 )
Brief. Bioinformatics - Learning transcriptional regulation on a genome scale: a theoretical analysis based on gene expression data. ( 0,790715969094305 )
AMIA Annu Symp Proc - An ontology-neutral framework for enrichment analysis. ( 0,79011036719246 )
AMIA Annu Symp Proc - Towards mechanism classifiers: expression-anchored Gene Ontology signature predicts clinical outcome in lung adenocarcinoma patients. ( 0,789821624177281 )
Comput Biol Chem - Sparse regularized discriminant analysis with application to microarrays. ( 0,787449424752602 )
Comput Math Methods Med - Identification and functional annotation of genome-wide ER-regulated genes in breast cancer based on ChIP-Seq data. ( 0,786607877513805 )
J. Comput. Biol. - Narratives in the network: interactive methods for mining cell signaling networks. ( 0,785970591313311 )
Brief. Bioinformatics - Literature-aided interpretation of gene expression data with the weighted global test. ( 0,782219623540753 )
Wiley Interdiscip Rev Syst Biol Med - Understanding multimodal biological decisions from single cell and population dynamics. ( 0,781716361350457 )
Comput Biol Chem - GPEC: a Cytoscape plug-in for random walk-based gene prioritization and biomedical evidence collection. ( 0,781015728012901 )
Methods Inf Med - Identification of breast cancer prognosis markers using integrative sparse boosting. ( 0,779962168344403 )
Wiley Interdiscip Rev Syst Biol Med - Bioimage informatics for understanding spatiotemporal dynamics of cellular processes. ( 0,77974530736065 )
J Biomed Inform - Structural network analysis of biological networks for assessment of potential disease model organisms. ( 0,77951613854969 )