Comput Math Methods Med - Integrating gene expression and protein interaction data for signaling pathway prediction of Alzheimer's disease.

Tópicos

{ gene(2352) biolog(1181) express(1162) }
{ model(2341) predict(2261) use(1141) }
{ data(1714) softwar(1251) tool(1186) }
{ import(1318) role(1303) understand(862) }
{ activ(1452) weight(1219) physic(1104) }
{ risk(3053) factor(974) diseas(938) }
{ sampl(1606) size(1419) use(1276) }
{ can(774) often(719) complex(702) }
{ system(1976) rule(880) can(841) }
{ measur(2081) correl(1212) valu(896) }
{ network(2748) neural(1063) input(814) }
{ chang(1828) time(1643) increas(1301) }
{ method(984) reconstruct(947) comput(926) }
{ estim(2440) model(1874) function(577) }
{ imag(2830) propos(1344) filter(1198) }
{ patient(2315) diseas(1263) diabet(1191) }
{ motion(1329) object(1292) video(1091) }
{ algorithm(1844) comput(1787) effici(935) }
{ care(1570) inform(1187) nurs(1089) }
{ studi(1410) differ(1259) use(1210) }
{ studi(1119) effect(1106) posit(819) }
{ blood(1257) pressur(1144) flow(957) }
{ research(1218) medic(880) student(794) }
{ signal(2180) analysi(812) frequenc(800) }
{ first(2504) two(1366) second(1323) }
{ activ(1138) subject(705) human(624) }
{ structur(1116) can(940) graph(676) }
{ drug(1928) target(777) effect(648) }
{ result(1111) use(1088) new(759) }
{ 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) }
{ imag(1057) registr(996) error(939) }
{ bind(1733) structur(1185) ligand(1036) }
{ sequenc(1873) structur(1644) protein(1328) }
{ method(1219) similar(1157) match(930) }
{ featur(3375) classif(2383) classifi(1994) }
{ imag(2675) segment(2577) method(1081) }
{ take(945) account(800) differ(722) }
{ studi(2440) review(1878) systemat(933) }
{ assess(1506) score(1403) qualiti(1306) }
{ treatment(1704) effect(941) patient(846) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ framework(1458) process(801) describ(734) }
{ problem(2511) optim(1539) algorithm(950) }
{ error(1145) method(1030) estim(1020) }
{ learn(2355) train(1041) set(1003) }
{ concept(1167) ontolog(924) domain(897) }
{ clinic(1479) use(1117) guidelin(835) }
{ 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) }
{ featur(1941) imag(1645) propos(1176) }
{ case(1353) use(1143) diagnosi(1136) }
{ howev(809) still(633) remain(590) }
{ data(3963) clinic(1234) research(1004) }
{ perform(999) metric(946) measur(919) }
{ research(1085) discuss(1038) issu(1018) }
{ system(1050) medic(1026) inform(1018) }
{ visual(1396) interact(850) tool(830) }
{ compound(1573) activ(1297) structur(1058) }
{ perform(1367) use(1326) method(1137) }
{ 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) }
{ state(1844) use(1261) util(961) }
{ 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) }
{ 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) }
{ 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) }
{ cancer(2502) breast(956) screen(824) }
{ use(976) code(926) identifi(902) }
{ use(1733) differ(960) four(931) }
{ implement(1333) system(1263) develop(1122) }
{ survey(1388) particip(1329) question(1065) }
{ process(1125) use(805) approach(778) }
{ method(1969) cluster(1462) data(1082) }
{ method(2212) result(1239) propos(1039) }

Resumo

Discovering the signaling pathway and regulatory network would provide significant advance in genome-wide understanding of pathogenesis of human diseases. Despite the rich transcriptome data, the limitation for microarray data is unable to detect changes beyond transcriptional level and insufficient in reconstructing pathways and regulatory networks. In our study, protein-protein interaction (PPI) data is introduced to add molecular biological information for predicting signaling pathway of Alzheimer's disease (AD). Combining PPI with gene expression data, significant genes are selected by modified linear regression model firstly. Then, according to the biological researches that inflammation reaction plays an important role in the generation and deterioration of AD, NF- B (nuclear factor-kappa B), as a significant inflammatory factor, has been selected as the beginning gene of the predicting signaling pathway. Based on that, integer linear programming (ILP) model is proposed to reconstruct the signaling pathway between NF- B and AD virulence gene APP (amyloid precursor protein). The results identify 6 AD virulence genes included in the predicted inflammatory signaling pathway, and a large amount of molecular biological analysis shows the great understanding of the underlying biological process of AD.

Resumo Limpo

discov signal pathway regulatori network provid signific advanc genomewid understand pathogenesi human diseas despit rich transcriptom data limit microarray data unabl detect chang beyond transcript level insuffici reconstruct pathway regulatori network studi proteinprotein interact ppi data introduc add molecular biolog inform predict signal pathway alzheim diseas ad combin ppi gene express data signific gene select modifi linear regress model first accord biolog research inflamm reaction play import role generat deterior ad nf b nuclear factorkappa b signific inflammatori factor select begin gene predict signal pathway base integ linear program ilp model propos reconstruct signal pathway nf b ad virul gene app amyloid precursor protein result identifi ad virul gene includ predict inflammatori signal pathway larg amount molecular biolog analysi show great understand under biolog process ad

Resumos Similares

Brief. Bioinformatics - Revealing the architecture of genetic and epigenetic regulation: a maximum likelihood model. ( 0,936878426779439 )
J. Comput. Biol. - Bioinformatics method to analyze the mechanism of pancreatic cancer disorder. ( 0,934161106764924 )
Wiley Interdiscip Rev Syst Biol Med - Diverse functional networks of Tbx3 in development and disease. ( 0,928014747501109 )
J Am Med Inform Assoc - Extracting coordinated patterns of DNA methylation and gene expression in ovarian cancer. ( 0,926822757847739 )
Comput. Biol. Med. - Degrees of separation as a statistical tool for evaluating candidate genes. ( 0,916756056988058 )
J Am Med Inform Assoc - Identifying disease genes and module biomarkers by differential interactions. ( 0,912971816470688 )
Comput. Biol. Med. - Identification and analysis of the regulatory network of Myc and microRNAs from high-throughput experimental data. ( 0,912480882971642 )
J Integr Bioinform - An integrative bioinformatics framework for genome-scale multiple level network reconstruction of rice. ( 0,911907603826693 )
Artif Intell Med - Identifying regulatory relationships among genomic loci, biological pathways, and disease. ( 0,905275460507135 )
Comput. Biol. Med. - Mathematical modeling and sensitivity analysis of the integrated TNFa-mediated apoptotic pathway for identifying key regulators. ( 0,902604359709183 )
Brief. Bioinformatics - Identifying miRNAs, targets and functions. ( 0,901797063549322 )
Comput Biol Chem - Disruption of murine Tcte3-3 induces tissue specific apoptosis via co-expression of Anxa5 and Pebp1. ( 0,900740219402892 )
J Integr Bioinform - Towards prediction and prioritization of disease genes by the modularity of human phenome-genome assembled network. ( 0,899439243088973 )
J Am Med Inform Assoc - Knowledge boosting: a graph-based integration approach with multi-omics data and genomic knowledge for cancer clinical outcome prediction. ( 0,898312883276446 )
J Am Med Inform Assoc - Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseases. ( 0,898149621734785 )
J. Comput. Biol. - A topology-based score for pathway enrichment. ( 0,897914319235858 )
J Biomed Inform - A comparative study of covariance selection models for the inference of gene regulatory networks. ( 0,89761184346881 )
Wiley Interdiscip Rev Syst Biol Med - Signaling networks in palate development. ( 0,8960373448336 )
J Am Med Inform Assoc - An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer. ( 0,89567449570929 )
J Biomed Inform - The detection of risk pathways, regulated by miRNAs, via the integration of sample-matched miRNA-mRNA profiles and pathway structure. ( 0,894968424372109 )
Comput Math Methods Med - Understanding the pathogenesis of Kawasaki disease by network and pathway analysis. ( 0,893448275967861 )
J. Comput. Biol. - Vavien: an algorithm for prioritizing candidate disease genes based on topological similarity of proteins in interaction networks. ( 0,893435066529467 )
J Integr Bioinform - Predicting breast cancer chemotherapeutic response using a novel tool for microarray data analysis. ( 0,891733622788994 )
Wiley Interdiscip Rev Syst Biol Med - miRNA regulation in the context of functional protein networks: principles and applications. ( 0,891183421021581 )
J Integr Bioinform - Network expansion and pathway enrichment analysis towards biologically significant findings from microarrays. ( 0,890958518169396 )
Wiley Interdiscip Rev Syst Biol Med - Recent advances in prostate development and links to prostatic diseases. ( 0,889847046026701 )
J Integr Bioinform - Knowledge enrichment analysis for human tissue-specific genes uncover new biological insights. ( 0,889785273167604 )
Wiley Interdiscip Rev Syst Biol Med - Postgenomic technologies targeting the Wnt signaling network. ( 0,88807893767871 )
J. Comput. Biol. - An algorithm for efficient identification of branched metabolic pathways. ( 0,883798697723701 )
Comput Math Methods Med - First comprehensive in silico analysis of the functional and structural consequences of SNPs in human GalNAc-T1 gene. ( 0,882952380432224 )
Wiley Interdiscip Rev Syst Biol Med - Systems biology of adipose tissue metabolism: regulation of growth, signaling and inflammation. ( 0,882403675516258 )
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. ( 0,880700721315997 )
Wiley Interdiscip Rev Syst Biol Med - Using variability in gene expression as a tool for studying gene regulation. ( 0,879658844117977 )
J Integr Bioinform - Assembling cell context-specific gene sets: a case in cardiomyopathy. ( 0,879026024796232 )
Artif Intell Med - An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods. ( 0,878601898549533 )
Brief. Bioinformatics - Targeted metabolic reconstruction: a novel approach for the characterization of plant-pathogen interactions. ( 0,876764726335719 )
Int J Med Inform - Translating genome wide association study results to associations among common diseases: in silico study with an electronic medical record. ( 0,875602345707517 )
J Biomed Inform - Prioritization of potential candidate disease genes by topological similarity of protein-protein interaction network and phenotype data. ( 0,875413829257401 )
Brief. Bioinformatics - Identification of aberrant pathways and network activities from high-throughput data. ( 0,872978762806032 )
J Integr Bioinform - A study of the short and long-term regulation of E. coli metabolic pathways. ( 0,866621091946216 )
Comput Biol Chem - Expression patterns of photoperiod and temperature regulated heading date genes in Oryza sativa. ( 0,864265517796908 )
Comput Biol Chem - Identifying novel prostate cancer associated pathways based on integrative microarray data analysis. ( 0,863019151205121 )
Wiley Interdiscip Rev Syst Biol Med - Reverse-engineering human regulatory networks. ( 0,86248869203413 )
J Am Med Inform Assoc - Complex-disease networks of trait-associated single-nucleotide polymorphisms (SNPs) unveiled by information theory. ( 0,861847767815409 )
J Biomed Inform - Comparative analysis of a novel disease phenotype network based on clinical manifestations. ( 0,861711046419345 )
Wiley Interdiscip Rev Syst Biol Med - Integrating omics into the cardiac differentiation of human pluripotent stem cells. ( 0,861036450650641 )
J Biomed Inform - Gene pathways and subnetworks distinguish between major glioma subtypes and elucidate potential underlying biology. ( 0,860532972731421 )
Wiley Interdiscip Rev Syst Biol Med - Using a systems biology approach to understand and study the mechanisms of metastasis. ( 0,86038498426267 )
Wiley Interdiscip Rev Syst Biol Med - Regulatory variation: an emerging vantage point for cancer biology. ( 0,859877947892861 )
Wiley Interdiscip Rev Syst Biol Med - Sex and the circuitry: progress toward a systems-level understanding of vertebrate sex determination. ( 0,859877369251513 )
Comput Biol Chem - Bioinformatic analysis of molecular network of glucosinolate biosynthesis. ( 0,855066827136895 )
AMIA Annu Symp Proc - Mining disease fingerprints from within genetic pathways. ( 0,854764382205392 )
Comput. Biol. Med. - Revealing pathway maps of renal cell carcinoma by gene expression change. ( 0,854620320530289 )
Wiley Interdiscip Rev Syst Biol Med - Network biology: a direct approach to study biological function. ( 0,853282477796489 )
Sci Data - DNA methylation temporal profiling following peripheral versus central nervous system axotomy. ( 0,849342774063414 )
Comput. Biol. Med. - A review on the computational approaches for gene regulatory network construction. ( 0,849088177788512 )
Wiley Interdiscip Rev Syst Biol Med - Stem cell bioengineering at the interface of systems-based models and high-throughput platforms. ( 0,848230219480219 )
Brief. Bioinformatics - Apoptosis regulatory protein-protein interaction demonstrates hierarchical scale-free fractal network. ( 0,848221105916551 )
Comput Biol Chem - Using volcano plots and regularized-chi statistics in genetic association studies. ( 0,847986974778108 )
Comput. Biol. Med. - A molecular prospective provides new insights into implication of PDYN and OPRK1 genes in alcohol dependence. ( 0,847880729596052 )
Comput Biol Chem - Large-scale mining co-expressed genes in Arabidopsis anther: from pair to group. ( 0,846603582677527 )
J Biomed Inform - Inferring cell cycle feedback regulation from gene expression data. ( 0,845899455970641 )
Methods Inf Med - Identification of breast cancer prognosis markers using integrative sparse boosting. ( 0,845339186255578 )
Wiley Interdiscip Rev Syst Biol Med - Cardiac function and disease: emerging role of small ubiquitin-related modifier. ( 0,844316643933741 )
Comput Biol Chem - Using gene expression programming to infer gene regulatory networks from time-series data. ( 0,842852314287181 )
Wiley Interdiscip Rev Syst Biol Med - Cyclic nucleotide signaling in intestinal epithelia: getting to the gut of the matter. ( 0,842427826978386 )
IEEE J Biomed Health Inform - Using evolutional properties of gene networks in understanding survival prognosis of glioblastoma. ( 0,840937207065513 )
J. Comput. Biol. - Computational disease gene prioritization: an appraisal. ( 0,840632782608534 )
Brief. Bioinformatics - Towards a comprehensive picture of the genetic landscape of complex traits. ( 0,840419617451364 )
Methods Inf Med - Pathway based microarray analysis, utilising enzyme compounds and cascade events. ( 0,839148081084466 )
Comput Biol Chem - GPEC: a Cytoscape plug-in for random walk-based gene prioritization and biomedical evidence collection. ( 0,839115527374744 )
Comput Biol Chem - A computational method of predicting regulatory interactions in Arabidopsis based on gene expression data and sequence information. ( 0,837665481556504 )
Comput. Biol. Med. - Meta analysis of gene expression changes upon treatment of A549 cells with anti-cancer drugs to identify universal responses. ( 0,836390496044242 )
J Am Med Inform Assoc - Utility of gene-specific algorithms for predicting pathogenicity of uncertain gene variants. ( 0,834134140773477 )
J Biomed Inform - Independent component analysis: mining microarray data for fundamental human gene expression modules. ( 0,832733705683161 )
Brief. Bioinformatics - Evolution of gene regulation--on the road towards computational inferences. ( 0,831458694528799 )
Brief. Bioinformatics - Learning transcriptional regulation on a genome scale: a theoretical analysis based on gene expression data. ( 0,829312657279961 )
Comput. Biol. Med. - Network-based approach reveals Y chromosome influences prostate cancer susceptibility. ( 0,829210378791616 )
Comput Biol Chem - Statistical analysis of combinatorial transcriptional regulatory motifs in human intron-containing promoter sequences. ( 0,827230141481128 )
Sci Data - Transcriptomic analysis of midbrain and individual hindbrain rhombomeres in the chick embryo. ( 0,824795576252528 )
Curr Protoc Bioinformatics - BEDTools: The Swiss-Army Tool for Genome Feature Analysis. ( 0,824786241371186 )
Wiley Interdiscip Rev Syst Biol Med - Noncoding RNAs in gene regulation. ( 0,823818709122823 )
Wiley Interdiscip Rev Syst Biol Med - Engineered genetic information processing circuits. ( 0,822070415694618 )
Wiley Interdiscip Rev Syst Biol Med - Bioimage informatics for understanding spatiotemporal dynamics of cellular processes. ( 0,82171452100528 )
AMIA Annu Symp Proc - Towards mechanism classifiers: expression-anchored Gene Ontology signature predicts clinical outcome in lung adenocarcinoma patients. ( 0,821704332375961 )
Comput Math Methods Med - Dynamic regulatory network reconstruction for Alzheimer's disease based on matrix decomposition techniques. ( 0,820452892588274 )
AMIA Annu Symp Proc - An ontology-neutral framework for enrichment analysis. ( 0,820419422637292 )
J Biomed Inform - Protein interaction network underpins concordant prognosis among heterogeneous breast cancer signatures. ( 0,819945363016348 )
Wiley Interdiscip Rev Syst Biol Med - Protein microarrays for genome-wide posttranslational modification analysis. ( 0,819137055271198 )
Wiley Interdiscip Rev Syst Biol Med - Where gene discovery turns into systems biology: genome-scale RNAi screens in Drosophila. ( 0,818942976620331 )
Comput. Biol. Med. - Discovering the transcriptional modules using microarray data by penalized matrix decomposition. ( 0,817839732319666 )
Comput Biol Chem - Gene expression patterns combined with bioinformatics analysis identify genes associated with cholangiocarcinoma. ( 0,816807337527574 )
Brief. Bioinformatics - Combining multidimensional genomic measurements for predicting cancer prognosis: observations from TCGA. ( 0,812864607974556 )
Sci Data - Genomes and phenomes of a population of outbred rats and its progenitors. ( 0,812123781854026 )
Wiley Interdiscip Rev Syst Biol Med - Understanding multimodal biological decisions from single cell and population dynamics. ( 0,810120730866731 )
Comput. Biol. Med. - Computational gene network study on antibiotic resistance genes of Acinetobacter baumannii. ( 0,807792044740706 )
Comput Biol Chem - Sparse regularized discriminant analysis with application to microarrays. ( 0,807680726028384 )
Comput Math Methods Med - Identification and functional annotation of genome-wide ER-regulated genes in breast cancer based on ChIP-Seq data. ( 0,806018756757267 )
Comput Biol Chem - Deciphering histone code of transcriptional regulation in malaria parasites by large-scale data mining. ( 0,805436290338693 )
J Am Med Inform Assoc - Using systems and structure biology tools to dissect cellular phenotypes. ( 0,805208139281537 )