J Biomed Inform - Gene pathways and subnetworks distinguish between major glioma subtypes and elucidate potential underlying biology.

Tópicos

{ gene(2352) biolog(1181) express(1162) }
{ featur(3375) classif(2383) classifi(1994) }
{ compound(1573) activ(1297) structur(1058) }
{ chang(1828) time(1643) increas(1301) }
{ result(1111) use(1088) new(759) }
{ case(1353) use(1143) diagnosi(1136) }
{ howev(809) still(633) remain(590) }
{ state(1844) use(1261) util(961) }
{ error(1145) method(1030) estim(1020) }
{ concept(1167) ontolog(924) domain(897) }
{ studi(1119) effect(1106) posit(819) }
{ cancer(2502) breast(956) screen(824) }
{ method(1219) similar(1157) match(930) }
{ network(2748) neural(1063) input(814) }
{ patient(2315) diseas(1263) diabet(1191) }
{ assess(1506) score(1403) qualiti(1306) }
{ method(1557) propos(1049) approach(1037) }
{ import(1318) role(1303) understand(862) }
{ visual(1396) interact(850) tool(830) }
{ data(3008) multipl(1320) sourc(1022) }
{ implement(1333) system(1263) develop(1122) }
{ activ(1452) weight(1219) physic(1104) }
{ model(2220) cell(1177) simul(1124) }
{ data(3963) clinic(1234) research(1004) }
{ model(2656) set(1616) predict(1553) }
{ data(2317) use(1299) case(1017) }
{ sampl(1606) size(1419) use(1276) }
{ structur(1116) can(940) graph(676) }
{ use(1733) differ(960) four(931) }
{ estim(2440) model(1874) function(577) }
{ decis(3086) make(1611) patient(1517) }
{ model(3404) distribut(989) bayesian(671) }
{ can(774) often(719) complex(702) }
{ imag(1947) propos(1133) code(1026) }
{ data(1737) use(1416) pattern(1282) }
{ 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) }
{ imag(2830) propos(1344) filter(1198) }
{ imag(2675) segment(2577) method(1081) }
{ take(945) account(800) differ(722) }
{ studi(2440) review(1878) systemat(933) }
{ motion(1329) object(1292) video(1091) }
{ treatment(1704) effect(941) patient(846) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ framework(1458) process(801) describ(734) }
{ problem(2511) optim(1539) algorithm(950) }
{ learn(2355) train(1041) set(1003) }
{ clinic(1479) use(1117) guidelin(835) }
{ algorithm(1844) comput(1787) effici(935) }
{ extract(1171) text(1153) clinic(932) }
{ data(1714) softwar(1251) tool(1186) }
{ 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) }
{ studi(1410) differ(1259) use(1210) }
{ risk(3053) factor(974) diseas(938) }
{ perform(999) metric(946) measur(919) }
{ research(1085) discuss(1038) issu(1018) }
{ 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) }
{ monitor(1329) mobil(1314) devic(1160) }
{ ehr(2073) health(1662) electron(1139) }
{ research(1218) medic(880) student(794) }
{ patient(2837) hospit(1953) medic(668) }
{ 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) }
{ first(2504) two(1366) second(1323) }
{ 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) }
{ health(1844) social(1437) communiti(874) }
{ high(1669) rate(1365) level(1280) }
{ use(976) code(926) identifi(902) }
{ drug(1928) target(777) effect(648) }
{ survey(1388) particip(1329) question(1065) }
{ process(1125) use(805) approach(778) }
{ method(1969) cluster(1462) data(1082) }
{ method(2212) result(1239) propos(1039) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

Molecular diagnostic tools are increasingly being used in an attempt to classify primary human brain tumors more accurately. While methods that are based on the analysis of individual gene expression prove to be useful for diagnostic purposes, they are devoid of biological significance since tumorgenesis is a concerted deregulation of multiple pathways rather than single genes. In a proof of concept, we utilize two large clinical data sets and show that the elucidation of enriched pathways and small differentially expressed sub-networks of protein interactions allow a reliable classification of glioblastomas and oligodendrogliomas. Applying a feature selection method, we observe that an optimized subset of pathways and subnetworks significantly improves the prediction accuracy. By determining the enrichment of altered genes in pathways and subnetworks we show that optimized subsets of genes rarely seem to be a target of genomic alteration. Our results suggest that groups of genes play a decisive role for the phenotype of the underlying tumor samples that can be utilized to reliably distinguish tumor types. In the absence of enrichment of genes that are genomically altered we assume that genetic changes largely exert an indirect rather than direct regulatory influence on a number of tumor-defining regulatory networks.

Resumo Limpo

molecular diagnost tool increas use attempt classifi primari human brain tumor accur method base analysi individu gene express prove use diagnost purpos devoid biolog signific sinc tumorgenesi concert deregul multipl pathway rather singl gene proof concept util two larg clinic data set show elucid enrich pathway small differenti express subnetwork protein interact allow reliabl classif glioblastoma oligodendroglioma appli featur select method observ optim subset pathway subnetwork signific improv predict accuraci determin enrich alter gene pathway subnetwork show optim subset gene rare seem target genom alter result suggest group gene play decis role phenotyp under tumor sampl can util reliabl distinguish tumor type absenc enrich gene genom alter assum genet chang larg exert indirect rather direct regulatori influenc number tumordefin regulatori network

Resumos Similares

J Integr Bioinform - Assembling cell context-specific gene sets: a case in cardiomyopathy. ( 0,894673843756445 )
Brief. Bioinformatics - Revealing the architecture of genetic and epigenetic regulation: a maximum likelihood model. ( 0,888149275937207 )
J. Comput. Biol. - Bioinformatics method to analyze the mechanism of pancreatic cancer disorder. ( 0,886964424154919 )
J Am Med Inform Assoc - Extracting coordinated patterns of DNA methylation and gene expression in ovarian cancer. ( 0,885732472464619 )
Comput Biol Chem - Disruption of murine Tcte3-3 induces tissue specific apoptosis via co-expression of Anxa5 and Pebp1. ( 0,882590948454269 )
J Integr Bioinform - Towards prediction and prioritization of disease genes by the modularity of human phenome-genome assembled network. ( 0,881434571340958 )
Wiley Interdiscip Rev Syst Biol Med - Using a systems biology approach to understand and study the mechanisms of metastasis. ( 0,880992628473213 )
J Integr Bioinform - Network expansion and pathway enrichment analysis towards biologically significant findings from microarrays. ( 0,880938420875132 )
Wiley Interdiscip Rev Syst Biol Med - Diverse functional networks of Tbx3 in development and disease. ( 0,879410302063846 )
J Biomed Inform - Prioritization of potential candidate disease genes by topological similarity of protein-protein interaction network and phenotype data. ( 0,8764174706842 )
J Am Med Inform Assoc - Identifying disease genes and module biomarkers by differential interactions. ( 0,876284598617746 )
Brief. Bioinformatics - Identification of aberrant pathways and network activities from high-throughput data. ( 0,876190035292486 )
Comput Math Methods Med - First comprehensive in silico analysis of the functional and structural consequences of SNPs in human GalNAc-T1 gene. ( 0,87471514007745 )
Comput. Biol. Med. - Identification and analysis of the regulatory network of Myc and microRNAs from high-throughput experimental data. ( 0,874171089945282 )
J Am Med Inform Assoc - Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseases. ( 0,872657261471611 )
J Integr Bioinform - An integrative bioinformatics framework for genome-scale multiple level network reconstruction of rice. ( 0,870204349665271 )
J Integr Bioinform - Knowledge enrichment analysis for human tissue-specific genes uncover new biological insights. ( 0,869278600155988 )
J Am Med Inform Assoc - Complex-disease networks of trait-associated single-nucleotide polymorphisms (SNPs) unveiled by information theory. ( 0,867030433219045 )
Wiley Interdiscip Rev Syst Biol Med - Systems biology of adipose tissue metabolism: regulation of growth, signaling and inflammation. ( 0,865105313403658 )
J. Comput. Biol. - An algorithm for efficient identification of branched metabolic pathways. ( 0,864741062565387 )
Comput Math Methods Med - Integrating gene expression and protein interaction data for signaling pathway prediction of Alzheimer's disease. ( 0,860532972731421 )
Artif Intell Med - Identifying regulatory relationships among genomic loci, biological pathways, and disease. ( 0,860159913187406 )
Wiley Interdiscip Rev Syst Biol Med - Regulatory variation: an emerging vantage point for cancer biology. ( 0,860032723920703 )
Sci Data - DNA methylation temporal profiling following peripheral versus central nervous system axotomy. ( 0,859305072419429 )
Methods Inf Med - Pathway based microarray analysis, utilising enzyme compounds and cascade events. ( 0,859077821026912 )
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. ( 0,859041690460959 )
Wiley Interdiscip Rev Syst Biol Med - Recent advances in prostate development and links to prostatic diseases. ( 0,85903917748972 )
Comput Biol Chem - Identifying novel prostate cancer associated pathways based on integrative microarray data analysis. ( 0,858216363561512 )
Wiley Interdiscip Rev Syst Biol Med - Postgenomic technologies targeting the Wnt signaling network. ( 0,858199422977951 )
Brief. Bioinformatics - Identifying miRNAs, targets and functions. ( 0,858027395636409 )
Comput. Biol. Med. - Mathematical modeling and sensitivity analysis of the integrated TNFa-mediated apoptotic pathway for identifying key regulators. ( 0,857309524678737 )
Comput Math Methods Med - Understanding the pathogenesis of Kawasaki disease by network and pathway analysis. ( 0,85587858236972 )
J. Comput. Biol. - A topology-based score for pathway enrichment. ( 0,854449850077411 )
J Am Med Inform Assoc - An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer. ( 0,853539062631719 )
J. Comput. Biol. - Vavien: an algorithm for prioritizing candidate disease genes based on topological similarity of proteins in interaction networks. ( 0,851477510477737 )
J Biomed Inform - Comparative analysis of a novel disease phenotype network based on clinical manifestations. ( 0,851321119224248 )
AMIA Annu Symp Proc - Mining disease fingerprints from within genetic pathways. ( 0,850165860149943 )
J Integr Bioinform - A study of the short and long-term regulation of E. coli metabolic pathways. ( 0,850023689904875 )
Comput. Biol. Med. - Degrees of separation as a statistical tool for evaluating candidate genes. ( 0,849510139140654 )
Wiley Interdiscip Rev Syst Biol Med - Signaling networks in palate development. ( 0,847535282919423 )
AMIA Annu Symp Proc - Towards mechanism classifiers: expression-anchored Gene Ontology signature predicts clinical outcome in lung adenocarcinoma patients. ( 0,844626215309 )
Comput Biol Chem - Expression patterns of photoperiod and temperature regulated heading date genes in Oryza sativa. ( 0,844294288257361 )
Comput Biol Chem - Using volcano plots and regularized-chi statistics in genetic association studies. ( 0,844065912898894 )
Wiley Interdiscip Rev Syst Biol Med - miRNA regulation in the context of functional protein networks: principles and applications. ( 0,843369504475836 )
J Biomed Inform - Systems-based biological concordance and predictive reproducibility of gene set discovery methods in cardiovascular disease. ( 0,842828923091157 )
IEEE J Biomed Health Inform - Using evolutional properties of gene networks in understanding survival prognosis of glioblastoma. ( 0,838929272347124 )
J Biomed Inform - The detection of risk pathways, regulated by miRNAs, via the integration of sample-matched miRNA-mRNA profiles and pathway structure. ( 0,83807434026843 )
Wiley Interdiscip Rev Syst Biol Med - Stem cell bioengineering at the interface of systems-based models and high-throughput platforms. ( 0,835777192941233 )
Comput. Biol. Med. - Revealing pathway maps of renal cell carcinoma by gene expression change. ( 0,835100858982829 )
J Am Med Inform Assoc - Knowledge boosting: a graph-based integration approach with multi-omics data and genomic knowledge for cancer clinical outcome prediction. ( 0,83459903755884 )
J Biomed Inform - Independent component analysis: mining microarray data for fundamental human gene expression modules. ( 0,834176078729575 )
Wiley Interdiscip Rev Syst Biol Med - Where gene discovery turns into systems biology: genome-scale RNAi screens in Drosophila. ( 0,83312000616464 )
Artif Intell Med - An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods. ( 0,83295851260671 )
Wiley Interdiscip Rev Syst Biol Med - Using variability in gene expression as a tool for studying gene regulation. ( 0,83197611201998 )
J Biomed Inform - Protein interaction network underpins concordant prognosis among heterogeneous breast cancer signatures. ( 0,831515908223481 )
Comput Biol Chem - Bioinformatic analysis of molecular network of glucosinolate biosynthesis. ( 0,829936398201183 )
Wiley Interdiscip Rev Syst Biol Med - Network biology: a direct approach to study biological function. ( 0,829679247361237 )
Wiley Interdiscip Rev Syst Biol Med - Reverse-engineering human regulatory networks. ( 0,827314257861673 )
Comput. Biol. Med. - Network-based approach reveals Y chromosome influences prostate cancer susceptibility. ( 0,827261474687606 )
Comput. Biol. Med. - A molecular prospective provides new insights into implication of PDYN and OPRK1 genes in alcohol dependence. ( 0,825832373040683 )
Comput Biol Chem - Statistical analysis of combinatorial transcriptional regulatory motifs in human intron-containing promoter sequences. ( 0,822003520358537 )
Comput Biol Chem - A computational method of predicting regulatory interactions in Arabidopsis based on gene expression data and sequence information. ( 0,821692004977358 )
Wiley Interdiscip Rev Syst Biol Med - Integrating omics into the cardiac differentiation of human pluripotent stem cells. ( 0,821501421212483 )
Comput Methods Programs Biomed - TC-VGC: a tumor classification system using variations in genes' correlation. ( 0,820909127967508 )
J. Comput. Biol. - Computational disease gene prioritization: an appraisal. ( 0,819365077846943 )
Sci Data - Transcriptomic analysis of midbrain and individual hindbrain rhombomeres in the chick embryo. ( 0,818859117806937 )
AMIA Annu Symp Proc - An ontology-neutral framework for enrichment analysis. ( 0,818291543894519 )
Wiley Interdiscip Rev Syst Biol Med - The zebrafish: scalable in vivo modeling for systems biology. ( 0,817320595496077 )
Comput Math Methods Med - Identification and functional annotation of genome-wide ER-regulated genes in breast cancer based on ChIP-Seq data. ( 0,816270808184798 )
J Biomed Inform - A comparative study of covariance selection models for the inference of gene regulatory networks. ( 0,815861536588098 )
Wiley Interdiscip Rev Syst Biol Med - Noncoding RNAs in gene regulation. ( 0,813636824398884 )
Wiley Interdiscip Rev Syst Biol Med - Decoding the functions of post-transcriptional regulators in the determination of inflammatory states: focus on macrophage activation. ( 0,812679229729536 )
J Biomed Inform - Inferring cell cycle feedback regulation from gene expression data. ( 0,811698280200934 )
Wiley Interdiscip Rev Syst Biol Med - Sex and the circuitry: progress toward a systems-level understanding of vertebrate sex determination. ( 0,810796967132786 )
Comput Biol Chem - In silico identification of conserved microRNAs and their target transcripts from expressed sequence tags of three earthworm species. ( 0,810769904066764 )
Brief. Bioinformatics - Learning transcriptional regulation on a genome scale: a theoretical analysis based on gene expression data. ( 0,809496351514015 )
J Biomed Inform - Structural network analysis of biological networks for assessment of potential disease model organisms. ( 0,807148537251947 )
Comput Biol Chem - Gene expression patterns combined with bioinformatics analysis identify genes associated with cholangiocarcinoma. ( 0,807031177708862 )
Comput. Biol. Med. - A review on the computational approaches for gene regulatory network construction. ( 0,806128753335036 )
J Am Med Inform Assoc - Advantages of genomic complexity: bioinformatics opportunities in microRNA cancer signatures. ( 0,805604825975131 )
Comput Biol Chem - Revealing weak differential gene expressions and their reproducible functions associated with breast cancer metastasis. ( 0,802825873526797 )
Comput Biol Chem - Using gene expression programming to infer gene regulatory networks from time-series data. ( 0,802119303937965 )
Curr Protoc Bioinformatics - BEDTools: The Swiss-Army Tool for Genome Feature Analysis. ( 0,801837564248583 )
Comput Biol Chem - GPEC: a Cytoscape plug-in for random walk-based gene prioritization and biomedical evidence collection. ( 0,801623884315537 )
Wiley Interdiscip Rev Syst Biol Med - Mediators and dynamics of DNA methylation. ( 0,801245633561162 )
Comput Biol Chem - Large-scale mining co-expressed genes in Arabidopsis anther: from pair to group. ( 0,800296687387441 )
J Am Med Inform Assoc - Utility of gene-specific algorithms for predicting pathogenicity of uncertain gene variants. ( 0,800094413031326 )
Wiley Interdiscip Rev Syst Biol Med - Genome-wide approaches in the study of microRNA biology. ( 0,799776716420261 )
Brief. Bioinformatics - Targeted metabolic reconstruction: a novel approach for the characterization of plant-pathogen interactions. ( 0,798785119210691 )
Brief. Bioinformatics - Apoptosis regulatory protein-protein interaction demonstrates hierarchical scale-free fractal network. ( 0,798471447911602 )
Methods Inf Med - Identification of breast cancer prognosis markers using integrative sparse boosting. ( 0,796701046817229 )
Comput. Biol. Med. - Computational gene network study on antibiotic resistance genes of Acinetobacter baumannii. ( 0,7966809071768 )
Wiley Interdiscip Rev Syst Biol Med - Understanding multimodal biological decisions from single cell and population dynamics. ( 0,796252872132236 )
Comput Biol Chem - Exploring the complexity of pathway-drug relationships using latent Dirichlet allocation. ( 0,795493647603345 )
Comput. Biol. Med. - Meta analysis of gene expression changes upon treatment of A549 cells with anti-cancer drugs to identify universal responses. ( 0,794603257560522 )
Comput. Biol. Med. - Discovering the transcriptional modules using microarray data by penalized matrix decomposition. ( 0,792920213013647 )
Sci Data - Genomes and phenomes of a population of outbred rats and its progenitors. ( 0,792795609992803 )
Comput Math Methods Med - Molecular signature of cancer at gene level or pathway level? Case studies of colorectal cancer and prostate cancer microarray data. ( 0,792056862589888 )
J. Comput. Biol. - Stochastic simulation of notch signaling reveals novel factors that mediate the differentiation of neural stem cells. ( 0,791539681560091 )
Wiley Interdiscip Rev Syst Biol Med - Cyclic nucleotide signaling in intestinal epithelia: getting to the gut of the matter. ( 0,790409479465357 )