Comput. Biol. Med. - Network-based approach reveals Y chromosome influences prostate cancer susceptibility.

Tópicos

{ gene(2352) biolog(1181) express(1162) }
{ import(1318) role(1303) understand(862) }
{ cancer(2502) breast(956) screen(824) }
{ sampl(1606) size(1419) use(1276) }
{ framework(1458) process(801) describ(734) }
{ error(1145) method(1030) estim(1020) }
{ search(2224) databas(1162) retriev(909) }
{ howev(809) still(633) remain(590) }
{ blood(1257) pressur(1144) flow(957) }
{ high(1669) rate(1365) level(1280) }
{ method(1969) cluster(1462) data(1082) }
{ method(984) reconstruct(947) comput(926) }
{ research(1085) discuss(1038) issu(1018) }
{ state(1844) use(1261) util(961) }
{ data(2317) use(1299) case(1017) }
{ result(1111) use(1088) new(759) }
{ chang(1828) time(1643) increas(1301) }
{ model(2220) cell(1177) simul(1124) }
{ general(901) number(790) one(736) }
{ data(3963) clinic(1234) research(1004) }
{ spatial(1525) area(1432) region(1030) }
{ data(3008) multipl(1320) sourc(1022) }
{ structur(1116) can(940) graph(676) }
{ use(976) code(926) identifi(902) }
{ activ(1452) weight(1219) physic(1104) }
{ can(774) often(719) complex(702) }
{ bind(1733) structur(1185) ligand(1036) }
{ featur(3375) classif(2383) classifi(1994) }
{ patient(2315) diseas(1263) diabet(1191) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ 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) }
{ method(1557) propos(1049) approach(1037) }
{ data(1714) softwar(1251) tool(1186) }
{ design(1359) user(1324) use(1319) }
{ control(1307) perform(991) simul(935) }
{ care(1570) inform(1187) nurs(1089) }
{ featur(1941) imag(1645) propos(1176) }
{ case(1353) use(1143) diagnosi(1136) }
{ studi(1410) differ(1259) use(1210) }
{ risk(3053) factor(974) diseas(938) }
{ perform(999) metric(946) measur(919) }
{ system(1050) medic(1026) inform(1018) }
{ 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) }
{ 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) }
{ model(2656) set(1616) predict(1553) }
{ 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) }
{ use(1733) differ(960) four(931) }
{ drug(1928) target(777) effect(648) }
{ implement(1333) system(1263) develop(1122) }
{ survey(1388) particip(1329) question(1065) }
{ estim(2440) model(1874) function(577) }
{ decis(3086) make(1611) patient(1517) }
{ process(1125) use(805) approach(778) }
{ method(2212) result(1239) propos(1039) }
{ 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) }
{ system(1976) rule(880) can(841) }
{ measur(2081) correl(1212) valu(896) }
{ imag(1057) registr(996) error(939) }
{ sequenc(1873) structur(1644) protein(1328) }
{ method(1219) similar(1157) match(930) }
{ 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) }
{ assess(1506) score(1403) qualiti(1306) }
{ treatment(1704) effect(941) patient(846) }

Resumo

The human Y chromosome contains a small number of genes that play a critical role in the determination of male-specific organs. Today's advances have provided valuable resources for defining the functions of this chromosome in both normal and cancerous prostates. Despite the fact that generation of high-throughput expression data is becoming usual; the systematic methods of data analysis in a biological context are still an impediment. Here we have shown that constructing co-expression networks using Y-chromosome genes provides an alternative strategy for the detection of new candidate genes involved in prostate cancer. In our approach, independent co-expression networks from normal and cancerous stages are reconstructed using a reverse engineering approach. We then highlight crucial pathways, biological processes, and genes involved in the prostate cancer by analyzing each network individually and in concert. Thus, we have identified 18 critical pathways and processes related to prostate cancer, many of which have previously been shown to be involved in cancer. In particular, we identify 22 Y-chromosome genes putatively linked to prostate cancer, 13 of which have been already verified experimentally. Our novel network-based approach is useful for accurate inference of processes and essential regulators that mediate molecular changes during cancer progression.

Resumo Limpo

human y chromosom contain small number gene play critic role determin malespecif organ today advanc provid valuabl resourc defin function chromosom normal cancer prostat despit fact generat highthroughput express data becom usual systemat method data analysi biolog context still impedi shown construct coexpress network use ychromosom gene provid altern strategi detect new candid gene involv prostat cancer approach independ coexpress network normal cancer stage reconstruct use revers engin approach highlight crucial pathway biolog process gene involv prostat cancer analyz network individu concert thus identifi critic pathway process relat prostat cancer mani previous shown involv cancer particular identifi ychromosom gene putat link prostat cancer alreadi verifi experiment novel networkbas approach use accur infer process essenti regul mediat molecular chang cancer progress

Resumos Similares

Wiley Interdiscip Rev Syst Biol Med - Regulatory variation: an emerging vantage point for cancer biology. ( 0,876361411752779 )
Brief. Bioinformatics - Identifying miRNAs, targets and functions. ( 0,874331653582232 )
J. Comput. Biol. - Bioinformatics method to analyze the mechanism of pancreatic cancer disorder. ( 0,869802857758414 )
J Biomed Inform - Inferring cell cycle feedback regulation from gene expression data. ( 0,864335729502322 )
Brief. Bioinformatics - Apoptosis regulatory protein-protein interaction demonstrates hierarchical scale-free fractal network. ( 0,864245381630095 )
Wiley Interdiscip Rev Syst Biol Med - Diverse functional networks of Tbx3 in development and disease. ( 0,862209785950292 )
Comput. Biol. Med. - A review on the computational approaches for gene regulatory network construction. ( 0,86055409437685 )
Comput. Biol. Med. - Genome-wide identification and structure-function studies of proteases and protease inhibitors in Cicer arietinum (chickpea). ( 0,860348574480968 )
J Am Med Inform Assoc - Extracting coordinated patterns of DNA methylation and gene expression in ovarian cancer. ( 0,858207765870762 )
Comput Math Methods Med - Understanding the pathogenesis of Kawasaki disease by network and pathway analysis. ( 0,855647932187954 )
J Biomed Inform - The detection of risk pathways, regulated by miRNAs, via the integration of sample-matched miRNA-mRNA profiles and pathway structure. ( 0,855403349662586 )
Comput. Biol. Med. - Mathematical modeling and sensitivity analysis of the integrated TNFa-mediated apoptotic pathway for identifying key regulators. ( 0,854912045094235 )
Wiley Interdiscip Rev Syst Biol Med - miRNA regulation in the context of functional protein networks: principles and applications. ( 0,854522027267843 )
J Integr Bioinform - Knowledge enrichment analysis for human tissue-specific genes uncover new biological insights. ( 0,851577974831985 )
J Biomed Inform - Protein interaction network underpins concordant prognosis among heterogeneous breast cancer signatures. ( 0,848220232701077 )
Comput Math Methods Med - Molecular signature of cancer at gene level or pathway level? Case studies of colorectal cancer and prostate cancer microarray data. ( 0,847836831665722 )
Comput Biol Chem - Disruption of murine Tcte3-3 induces tissue specific apoptosis via co-expression of Anxa5 and Pebp1. ( 0,847260498534346 )
Wiley Interdiscip Rev Syst Biol Med - Postgenomic technologies targeting the Wnt signaling network. ( 0,844969223382002 )
Brief. Bioinformatics - Towards a comprehensive picture of the genetic landscape of complex traits. ( 0,832081640915475 )
J Am Med Inform Assoc - Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseases. ( 0,830797634592709 )
Wiley Interdiscip Rev Syst Biol Med - Recent advances in prostate development and links to prostatic diseases. ( 0,829413899586542 )
Comput Math Methods Med - Integrating gene expression and protein interaction data for signaling pathway prediction of Alzheimer's disease. ( 0,829210378791616 )
J Integr Bioinform - Network expansion and pathway enrichment analysis towards biologically significant findings from microarrays. ( 0,82908411522091 )
Brief. Bioinformatics - Revealing the architecture of genetic and epigenetic regulation: a maximum likelihood model. ( 0,828226107991342 )
Comput Math Methods Med - Identification and functional annotation of genome-wide ER-regulated genes in breast cancer based on ChIP-Seq data. ( 0,827603187584935 )
J Biomed Inform - Gene pathways and subnetworks distinguish between major glioma subtypes and elucidate potential underlying biology. ( 0,827261474687606 )
J Am Med Inform Assoc - Identifying disease genes and module biomarkers by differential interactions. ( 0,826346965599312 )
J Integr Bioinform - An integrative bioinformatics framework for genome-scale multiple level network reconstruction of rice. ( 0,824745136149318 )
J. Comput. Biol. - A topology-based score for pathway enrichment. ( 0,824036391406759 )
Wiley Interdiscip Rev Syst Biol Med - Cardiac function and disease: emerging role of small ubiquitin-related modifier. ( 0,823483632812401 )
Wiley Interdiscip Rev Syst Biol Med - Genome-wide approaches in the study of microRNA biology. ( 0,821438050522302 )
Wiley Interdiscip Rev Syst Biol Med - Bioimage informatics for understanding spatiotemporal dynamics of cellular processes. ( 0,819949943027505 )
Comput Math Methods Med - First comprehensive in silico analysis of the functional and structural consequences of SNPs in human GalNAc-T1 gene. ( 0,817785763975815 )
Comput. Biol. Med. - Revealing pathway maps of renal cell carcinoma by gene expression change. ( 0,817543947322474 )
J Biomed Inform - Prioritization of potential candidate disease genes by topological similarity of protein-protein interaction network and phenotype data. ( 0,816584912899741 )
Brief. Bioinformatics - Evolution of gene regulation--on the road towards computational inferences. ( 0,815383607482041 )
Comput. Biol. Med. - Identification and analysis of the regulatory network of Myc and microRNAs from high-throughput experimental data. ( 0,814742119310912 )
Comput. Biol. Med. - Learning the local Bayesian network structure around the ZNF217 oncogene in breast tumours. ( 0,812867203195366 )
Sci Data - DNA methylation temporal profiling following peripheral versus central nervous system axotomy. ( 0,812383500304475 )
Comput Biol Chem - Reconstruction and crosstalk of protein-protein interaction networks of Wnt and Hedgehog signaling in Drosophila melanogaster. ( 0,81194017109552 )
Med Biol Eng Comput - Cell sheet integrity and nanomechanical breakdown during programmed cell death. ( 0,810663624339143 )
Comput Biol Chem - In silico identification of conserved microRNAs and their target transcripts from expressed sequence tags of three earthworm species. ( 0,810125673316941 )
J Integr Bioinform - Assembling cell context-specific gene sets: a case in cardiomyopathy. ( 0,809600328689521 )
Comput Methods Programs Biomed - TMT-HCC: a tool for text mining the biomedical literature for hepatocellular carcinoma (HCC) biomarkers identification. ( 0,808367276340188 )
Wiley Interdiscip Rev Syst Biol Med - Using variability in gene expression as a tool for studying gene regulation. ( 0,807867886672808 )
Wiley Interdiscip Rev Syst Biol Med - Stem cell bioengineering at the interface of systems-based models and high-throughput platforms. ( 0,80713835951424 )
Wiley Interdiscip Rev Syst Biol Med - Noncoding RNAs in gene regulation. ( 0,802466283872498 )
Comput Methods Programs Biomed - TC-VGC: a tumor classification system using variations in genes' correlation. ( 0,802401190843213 )
Comput Biol Chem - Identifying novel prostate cancer associated pathways based on integrative microarray data analysis. ( 0,801573302163642 )
J. Comput. Biol. - An algorithm for efficient identification of branched metabolic pathways. ( 0,800831813214067 )
Methods Inf Med - Identification of breast cancer prognosis markers using integrative sparse boosting. ( 0,800581205550904 )
J. Comput. Biol. - Vavien: an algorithm for prioritizing candidate disease genes based on topological similarity of proteins in interaction networks. ( 0,800385351487227 )
Brief. Bioinformatics - Exploring the function of genetic variants in the non-coding genomic regions: approaches for identifying human regulatory variants affecting gene expression. ( 0,799300093131884 )
J Biomed Inform - Comparative analysis of a novel disease phenotype network based on clinical manifestations. ( 0,796894148073039 )
J Integr Bioinform - Integrating protein-protein interaction networks with gene-gene co-expression networks improves gene signatures for classifying breast cancer metastasis. ( 0,795070281256162 )
Artif Intell Med - Identifying regulatory relationships among genomic loci, biological pathways, and disease. ( 0,794470112182961 )
Wiley Interdiscip Rev Syst Biol Med - Establishing the stem cell state: insights from regulatory network analysis of blood stem cell development. ( 0,793346065225149 )
Comput Biol Chem - Prediction and verification of microRNAs related to proline accumulation under drought stress in potato. ( 0,791802516890178 )
Wiley Interdiscip Rev Syst Biol Med - Using a systems biology approach to understand and study the mechanisms of metastasis. ( 0,791562841329148 )
Comput Biol Chem - Large-scale mining co-expressed genes in Arabidopsis anther: from pair to group. ( 0,790964790477006 )
J Am Med Inform Assoc - An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer. ( 0,790013324136082 )
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. ( 0,788907924795945 )
J Integr Bioinform - A study of the short and long-term regulation of E. coli metabolic pathways. ( 0,788905792422934 )
J Integr Bioinform - Towards prediction and prioritization of disease genes by the modularity of human phenome-genome assembled network. ( 0,788633162307011 )
Wiley Interdiscip Rev Syst Biol Med - Systems biology of adipose tissue metabolism: regulation of growth, signaling and inflammation. ( 0,788215775528657 )
Brief. Bioinformatics - Identification of aberrant pathways and network activities from high-throughput data. ( 0,787559839540833 )
Wiley Interdiscip Rev Syst Biol Med - Signaling networks in palate development. ( 0,787304525358481 )
Comput. Biol. Med. - Impact of TGF-b on breast cancer from a quantitative proteomic analysis. ( 0,78638301354487 )
J Biomed Inform - Serum cancer biomarker discovery through analysis of gene expression data sets across multiple tumor and normal tissues. ( 0,786078067652981 )
J Am Med Inform Assoc - Advantages of genomic complexity: bioinformatics opportunities in microRNA cancer signatures. ( 0,784873433542321 )
Comput Biol Chem - Expression patterns of photoperiod and temperature regulated heading date genes in Oryza sativa. ( 0,78431700755795 )
Wiley Interdiscip Rev Syst Biol Med - Cyclic nucleotide signaling in intestinal epithelia: getting to the gut of the matter. ( 0,784066405397414 )
J Am Med Inform Assoc - Complex-disease networks of trait-associated single-nucleotide polymorphisms (SNPs) unveiled by information theory. ( 0,782593763413811 )
Wiley Interdiscip Rev Syst Biol Med - Reverse-engineering human regulatory networks. ( 0,78138368520314 )
Comput. Biol. Med. - Degrees of separation as a statistical tool for evaluating candidate genes. ( 0,779428530349166 )
Brief. Bioinformatics - Learning transcriptional regulation on a genome scale: a theoretical analysis based on gene expression data. ( 0,779190033744383 )
Sci Data - Transcriptomic analysis of midbrain and individual hindbrain rhombomeres in the chick embryo. ( 0,778162267904311 )
J. Comput. Biol. - Computational disease gene prioritization: an appraisal. ( 0,778022393459243 )
Comput Biol Chem - Using volcano plots and regularized-chi statistics in genetic association studies. ( 0,777914294767483 )
J Integr Bioinform - Predicting breast cancer chemotherapeutic response using a novel tool for microarray data analysis. ( 0,777906911417729 )
Wiley Interdiscip Rev Syst Biol Med - Network biology: a direct approach to study biological function. ( 0,777817459305202 )
Comput Biol Chem - Bioinformatic analysis of molecular network of glucosinolate biosynthesis. ( 0,776019736301992 )
AMIA Annu Symp Proc - Towards mechanism classifiers: expression-anchored Gene Ontology signature predicts clinical outcome in lung adenocarcinoma patients. ( 0,77489656034192 )
Comput Biol Chem - Detecting adaptive evolution and functional divergence in aminocyclopropane-1-carboxylate synthase (ACS) gene family. ( 0,77281127694443 )
Comput Biol Chem - Gene expression patterns combined with bioinformatics analysis identify genes associated with cholangiocarcinoma. ( 0,772190676912153 )
Comput Biol Chem - Revealing weak differential gene expressions and their reproducible functions associated with breast cancer metastasis. ( 0,771768291865956 )
Wiley Interdiscip Rev Syst Biol Med - Sex and the circuitry: progress toward a systems-level understanding of vertebrate sex determination. ( 0,770348998061676 )
Artif Intell Med - An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods. ( 0,768492718720366 )
Curr Protoc Bioinformatics - BEDTools: The Swiss-Army Tool for Genome Feature Analysis. ( 0,767253745782607 )
Wiley Interdiscip Rev Syst Biol Med - Understanding multimodal biological decisions from single cell and population dynamics. ( 0,764756481692592 )
Comput. Biol. Med. - A molecular prospective provides new insights into implication of PDYN and OPRK1 genes in alcohol dependence. ( 0,763398213763192 )
J Am Med Inform Assoc - Knowledge boosting: a graph-based integration approach with multi-omics data and genomic knowledge for cancer clinical outcome prediction. ( 0,763356071565478 )
J. Comput. Biol. - A stationary wavelet entropy-based clustering approach accurately predicts gene expression. ( 0,762447428565459 )
Sci Data - Genomes and phenomes of a population of outbred rats and its progenitors. ( 0,761843381811497 )
Comput Math Methods Med - Dynamic regulatory network reconstruction for Alzheimer's disease based on matrix decomposition techniques. ( 0,759063559140988 )
AMIA Annu Symp Proc - Mining disease fingerprints from within genetic pathways. ( 0,758423816765749 )
IEEE J Biomed Health Inform - Using evolutional properties of gene networks in understanding survival prognosis of glioblastoma. ( 0,755994099637313 )
J Biomed Inform - A comparative study of covariance selection models for the inference of gene regulatory networks. ( 0,755864152921728 )
Methods Inf Med - Pathway based microarray analysis, utilising enzyme compounds and cascade events. ( 0,755264575823887 )
Brief. Bioinformatics - Breast cancer classification: linking molecular mechanisms to disease prognosis. ( 0,755180130633063 )