J Biomed Inform - Where we stand, where we are moving: Surveying computational techniques for identifying miRNA genes and uncovering their regulatory role.

Tópicos

{ gene(2352) biolog(1181) express(1162) }
{ data(1737) use(1416) pattern(1282) }
{ research(1085) discuss(1038) issu(1018) }
{ can(774) often(719) complex(702) }
{ method(1557) propos(1049) approach(1037) }
{ concept(1167) ontolog(924) domain(897) }
{ inform(2794) health(2639) internet(1427) }
{ method(1219) similar(1157) match(930) }
{ framework(1458) process(801) describ(734) }
{ visual(1396) interact(850) tool(830) }
{ detect(2391) sensit(1101) algorithm(908) }
{ network(2748) neural(1063) input(814) }
{ howev(809) still(633) remain(590) }
{ import(1318) role(1303) understand(862) }
{ blood(1257) pressur(1144) flow(957) }
{ state(1844) use(1261) util(961) }
{ model(2656) set(1616) predict(1553) }
{ structur(1116) can(940) graph(676) }
{ imag(1057) registr(996) error(939) }
{ bind(1733) structur(1185) ligand(1036) }
{ imag(2675) segment(2577) method(1081) }
{ take(945) account(800) differ(722) }
{ motion(1329) object(1292) video(1091) }
{ problem(2511) optim(1539) algorithm(950) }
{ chang(1828) time(1643) increas(1301) }
{ algorithm(1844) comput(1787) effici(935) }
{ model(2220) cell(1177) simul(1124) }
{ data(3963) clinic(1234) research(1004) }
{ studi(1410) differ(1259) use(1210) }
{ risk(3053) factor(974) diseas(938) }
{ perform(999) metric(946) measur(919) }
{ compound(1573) activ(1297) structur(1058) }
{ cost(1906) reduc(1198) effect(832) }
{ sampl(1606) size(1419) use(1276) }
{ first(2504) two(1366) second(1323) }
{ intervent(3218) particip(2042) group(1664) }
{ time(1939) patient(1703) rate(768) }
{ high(1669) rate(1365) level(1280) }
{ use(976) code(926) identifi(902) }
{ use(1733) differ(960) four(931) }
{ activ(1452) weight(1219) physic(1104) }
{ model(3404) distribut(989) bayesian(671) }
{ imag(1947) propos(1133) code(1026) }
{ system(1976) rule(880) can(841) }
{ measur(2081) correl(1212) valu(896) }
{ sequenc(1873) structur(1644) protein(1328) }
{ featur(3375) classif(2383) classifi(1994) }
{ imag(2830) propos(1344) filter(1198) }
{ patient(2315) diseas(1263) diabet(1191) }
{ studi(2440) review(1878) systemat(933) }
{ assess(1506) score(1403) qualiti(1306) }
{ treatment(1704) effect(941) patient(846) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ error(1145) method(1030) estim(1020) }
{ learn(2355) train(1041) set(1003) }
{ clinic(1479) use(1117) guidelin(835) }
{ 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) }
{ case(1353) use(1143) diagnosi(1136) }
{ system(1050) medic(1026) inform(1018) }
{ model(2341) predict(2261) use(1141) }
{ perform(1367) use(1326) method(1137) }
{ studi(1119) effect(1106) posit(819) }
{ 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) }
{ data(2317) use(1299) case(1017) }
{ age(1611) year(1155) adult(843) }
{ medic(1828) order(1363) alert(1069) }
{ signal(2180) analysi(812) frequenc(800) }
{ group(2977) signific(1463) compar(1072) }
{ data(3008) multipl(1320) sourc(1022) }
{ activ(1138) subject(705) human(624) }
{ 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) }
{ 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) }
{ process(1125) use(805) approach(778) }
{ method(1969) cluster(1462) data(1082) }
{ method(2212) result(1239) propos(1039) }

Resumo

Traditional biology was forced to restate some of its principles when the microRNA (miRNA) genes and their regulatory role were firstly discovered. Typically, miRNAs are small non-coding RNA molecules which have the ability to bind to the 3'untraslated region (UTR) of their mRNA target genes for cleavage or translational repression. Existing experimental techniques for their identification and the prediction of the target genes share some important limitations such as low coverage, time consuming experiments and high cost reagents. Hence, many computational methods have been proposed for these tasks to overcome these limitations. Recently, many researchers emphasized on the development of computational approaches to predict the participation of miRNA genes in regulatory networks and to analyze their transcription mechanisms. All these approaches have certain advantages and disadvantages which are going to be described in the present survey. Our work is differentiated from existing review papers by updating the methodologies list and emphasizing on the computational issues that arise from the miRNA data analysis. Furthermore, in the present survey, the various miRNA data analysis steps are treated as an integrated procedure whose aims and scope is to uncover the regulatory role and mechanisms of the miRNA genes. This integrated view of the miRNA data analysis steps may be extremely useful for all researchers even if they work on just a single step.

Resumo Limpo

tradit biolog forc restat principl microrna mirna gene regulatori role first discov typic mirna small noncod rna molecul abil bind untrasl region utr mrna target gene cleavag translat repress exist experiment techniqu identif predict target gene share import limit low coverag time consum experi high cost reagent henc mani comput method propos task overcom limit recent mani research emphas develop comput approach predict particip mirna gene regulatori network analyz transcript mechan approach certain advantag disadvantag go describ present survey work differenti exist review paper updat methodolog list emphas comput issu aris mirna data analysi furthermor present survey various mirna data analysi step treat integr procedur whose aim scope uncov regulatori role mechan mirna gene integr view mirna data analysi step may extrem use research even work just singl step

Resumos Similares

Comput Biol Chem - Bioinformatic analysis of molecular network of glucosinolate biosynthesis. ( 0,798101943725857 )
Comput Biol Chem - Deciphering histone code of transcriptional regulation in malaria parasites by large-scale data mining. ( 0,793426704807397 )
J Am Med Inform Assoc - Identifying disease genes and module biomarkers by differential interactions. ( 0,782102732598532 )
Wiley Interdiscip Rev Syst Biol Med - The zebrafish: scalable in vivo modeling for systems biology. ( 0,781126641114085 )
Wiley Interdiscip Rev Syst Biol Med - Network biology: a direct approach to study biological function. ( 0,776309433453752 )
J Am Med Inform Assoc - Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseases. ( 0,776296369361042 )
Brief. Bioinformatics - Toward microRNA-mediated gene regulatory networks in plants. ( 0,77588974593592 )
Comput Biol Chem - Disruption of murine Tcte3-3 induces tissue specific apoptosis via co-expression of Anxa5 and Pebp1. ( 0,775742286402864 )
Brief. Bioinformatics - Identification of aberrant pathways and network activities from high-throughput data. ( 0,77417053811169 )
Wiley Interdiscip Rev Syst Biol Med - Using variability in gene expression as a tool for studying gene regulation. ( 0,773816106647099 )
Brief. Bioinformatics - Alternative applications for distinct RNA sequencing strategies. ( 0,772388100930176 )
J Am Med Inform Assoc - Complex-disease networks of trait-associated single-nucleotide polymorphisms (SNPs) unveiled by information theory. ( 0,769738270376104 )
Wiley Interdiscip Rev Syst Biol Med - Quantitative analysis of phosphorylation-based protein signaling networks in the immune system by mass spectrometry. ( 0,768592156307495 )
AMIA Annu Symp Proc - Similarity-based disease risk assessment for personal genomes: proof of concept. ( 0,768012992799453 )
Wiley Interdiscip Rev Syst Biol Med - Noncoding RNAs in gene regulation. ( 0,767692984197206 )
Wiley Interdiscip Rev Syst Biol Med - Mediators and dynamics of DNA methylation. ( 0,766829636265255 )
J Integr Bioinform - Network expansion and pathway enrichment analysis towards biologically significant findings from microarrays. ( 0,764080137527204 )
Brief. Bioinformatics - Revealing the architecture of genetic and epigenetic regulation: a maximum likelihood model. ( 0,762024388947122 )
J. Comput. Biol. - An algorithm for efficient identification of branched metabolic pathways. ( 0,761907013794501 )
Comput. Biol. Med. - A review on the computational approaches for gene regulatory network construction. ( 0,761178393773595 )
Brief. Bioinformatics - Literature-aided interpretation of gene expression data with the weighted global test. ( 0,761003375985344 )
Brief. Bioinformatics - Evolution of gene regulation--on the road towards computational inferences. ( 0,759244094234396 )
Comput. Biol. Med. - Degrees of separation as a statistical tool for evaluating candidate genes. ( 0,758751300566292 )
Wiley Interdiscip Rev Syst Biol Med - Genome network medicine: innovation to overcome huge challenges in cancer therapy. ( 0,755281425514487 )
J. Comput. Biol. - Biological network querying techniques: analysis and comparison. ( 0,75358862235216 )
J. Comput. Biol. - Vavien: an algorithm for prioritizing candidate disease genes based on topological similarity of proteins in interaction networks. ( 0,751261148293893 )
Comput Math Methods Med - First comprehensive in silico analysis of the functional and structural consequences of SNPs in human GalNAc-T1 gene. ( 0,75037497969538 )
Comput Biol Chem - Using volcano plots and regularized-chi statistics in genetic association studies. ( 0,749926945638985 )
Wiley Interdiscip Rev Syst Biol Med - Diverse functional networks of Tbx3 in development and disease. ( 0,747232850008337 )
AMIA Annu Symp Proc - An ontology-neutral framework for enrichment analysis. ( 0,745799582978213 )
AMIA Annu Symp Proc - Mining disease fingerprints from within genetic pathways. ( 0,745484400368038 )
Wiley Interdiscip Rev Syst Biol Med - Recent advances in prostate development and links to prostatic diseases. ( 0,745170739427572 )
J. Comput. Biol. - Computational disease gene prioritization: an appraisal. ( 0,745083642914598 )
Wiley Interdiscip Rev Syst Biol Med - Bioimage informatics for understanding spatiotemporal dynamics of cellular processes. ( 0,745028252538511 )
Brief. Bioinformatics - Learning transcriptional regulation on a genome scale: a theoretical analysis based on gene expression data. ( 0,743832162753379 )
J Am Med Inform Assoc - Extracting coordinated patterns of DNA methylation and gene expression in ovarian cancer. ( 0,743396999399811 )
Comput Biol Chem - Identifying novel prostate cancer associated pathways based on integrative microarray data analysis. ( 0,743300298888693 )
Wiley Interdiscip Rev Syst Biol Med - Systems biology of adipose tissue metabolism: regulation of growth, signaling and inflammation. ( 0,743073689089163 )
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. ( 0,742658030755473 )
Comput Biol Chem - Analysis of transcriptional synergy between upstream regions and introns in ribosomal protein genes of yeast. ( 0,739539283372804 )
J. Comput. Biol. - A topology-based score for pathway enrichment. ( 0,738556073161157 )
J Integr Bioinform - Towards prediction and prioritization of disease genes by the modularity of human phenome-genome assembled network. ( 0,737448962773574 )
J Am Med Inform Assoc - An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer. ( 0,73644735859062 )
Brief. Bioinformatics - Identifying miRNAs, targets and functions. ( 0,735844838195717 )
Comput. Biol. Med. - Identification and analysis of the regulatory network of Myc and microRNAs from high-throughput experimental data. ( 0,735692292690838 )
J Biomed Inform - Unraveling complex temporal associations in cellular systems across multiple time-series microarray datasets. ( 0,734929999202766 )
J Integr Bioinform - Knowledge enrichment analysis for human tissue-specific genes uncover new biological insights. ( 0,734571341117195 )
Wiley Interdiscip Rev Syst Biol Med - miRNA regulation in the context of functional protein networks: principles and applications. ( 0,734090892423046 )
Comput Math Methods Med - Understanding the pathogenesis of Kawasaki disease by network and pathway analysis. ( 0,733468018401961 )
J Biomed Inform - The detection of risk pathways, regulated by miRNAs, via the integration of sample-matched miRNA-mRNA profiles and pathway structure. ( 0,731869723059994 )
J Integr Bioinform - An integrative bioinformatics framework for genome-scale multiple level network reconstruction of rice. ( 0,730813379548769 )
Wiley Interdiscip Rev Syst Biol Med - Pharmacogenomics discovery and implementation in genome-wide association studies era. ( 0,729885627521781 )
Wiley Interdiscip Rev Syst Biol Med - Signaling networks in palate development. ( 0,72926452836991 )
Sci Data - DNA methylation temporal profiling following peripheral versus central nervous system axotomy. ( 0,728555615839795 )
J Biomed Inform - Gene pathways and subnetworks distinguish between major glioma subtypes and elucidate potential underlying biology. ( 0,728193370002292 )
Brief. Bioinformatics - Visualizing time-related data in biology, a review. ( 0,727730420446585 )
Artif Intell Med - Identifying regulatory relationships among genomic loci, biological pathways, and disease. ( 0,72632179671318 )
J. Comput. Biol. - Bioinformatics method to analyze the mechanism of pancreatic cancer disorder. ( 0,726170981526131 )
J Integr Bioinform - Assembling cell context-specific gene sets: a case in cardiomyopathy. ( 0,725726205871237 )
Comput Math Methods Med - Integrating gene expression and protein interaction data for signaling pathway prediction of Alzheimer's disease. ( 0,722959506955048 )
Wiley Interdiscip Rev Syst Biol Med - Postgenomic technologies targeting the Wnt signaling network. ( 0,722680082517479 )
Wiley Interdiscip Rev Syst Biol Med - Mechanisms controlling hematopoietic stem cell functions during normal hematopoiesis and hematological malignancies. ( 0,721856887682651 )
Comput Methods Programs Biomed - TMT-HCC: a tool for text mining the biomedical literature for hepatocellular carcinoma (HCC) biomarkers identification. ( 0,721529604776546 )
Comput Biol Chem - Gene expression patterns combined with bioinformatics analysis identify genes associated with cholangiocarcinoma. ( 0,72073555868644 )
Comput Biol Chem - Expression patterns of photoperiod and temperature regulated heading date genes in Oryza sativa. ( 0,720685979104722 )
Comput. Biol. Med. - Mathematical modeling and sensitivity analysis of the integrated TNFa-mediated apoptotic pathway for identifying key regulators. ( 0,719550118785141 )
Brief. Bioinformatics - Transcription factor and microRNA co-regulatory loops: important regulatory motifs in biological processes and diseases. ( 0,719024065698902 )
J Biomed Inform - Hemojuvelin-hepcidin axis modeled and analyzed using Petri nets. ( 0,718111031274002 )
Brief. Bioinformatics - How to cluster gene expression dynamics in response to environmental signals. ( 0,717900217958304 )
Comput. Biol. Med. - Using positive and negative patterns to extract information from journal articles regarding the regulation of a target gene by a transcription factor. ( 0,717533792772832 )
Wiley Interdiscip Rev Syst Biol Med - Stem cell bioengineering at the interface of systems-based models and high-throughput platforms. ( 0,717260069317055 )
J Am Med Inform Assoc - Advantages of genomic complexity: bioinformatics opportunities in microRNA cancer signatures. ( 0,715602389022557 )
Methods Inf Med - Pathway based microarray analysis, utilising enzyme compounds and cascade events. ( 0,715393721359265 )
Wiley Interdiscip Rev Syst Biol Med - Genome-wide approaches in the study of microRNA biology. ( 0,715058412470323 )
J Am Med Inform Assoc - Knowledge boosting: a graph-based integration approach with multi-omics data and genomic knowledge for cancer clinical outcome prediction. ( 0,714891762270676 )
Wiley Interdiscip Rev Syst Biol Med - Recent approaches to the prioritization of candidate disease genes. ( 0,711738463119954 )
J Biomed Inform - Comparative analysis of a novel disease phenotype network based on clinical manifestations. ( 0,711411147665711 )
Comput Biol Chem - Large-scale mining co-expressed genes in Arabidopsis anther: from pair to group. ( 0,711019154806757 )
Brief. Bioinformatics - Introduction into the analysis of high-throughput-sequencing based epigenome data. ( 0,710507801717282 )
IEEE J Biomed Health Inform - Using evolutional properties of gene networks in understanding survival prognosis of glioblastoma. ( 0,710406284978523 )
J Integr Bioinform - A study of the short and long-term regulation of E. coli metabolic pathways. ( 0,710072605148377 )
Brief. Bioinformatics - High-performance analysis of biological systems dynamics with the DiVinE model checker. ( 0,708593353365696 )
Wiley Interdiscip Rev Syst Biol Med - Where gene discovery turns into systems biology: genome-scale RNAi screens in Drosophila. ( 0,708189512523635 )
Comput Math Methods Med - Dynamic regulatory network reconstruction for Alzheimer's disease based on matrix decomposition techniques. ( 0,70683749248154 )
Wiley Interdiscip Rev Syst Biol Med - Cardiac function and disease: emerging role of small ubiquitin-related modifier. ( 0,705741449650258 )
Wiley Interdiscip Rev Syst Biol Med - Integrating omics into the cardiac differentiation of human pluripotent stem cells. ( 0,70448652875624 )
Wiley Interdiscip Rev Syst Biol Med - Sex and the circuitry: progress toward a systems-level understanding of vertebrate sex determination. ( 0,70422377406141 )
J. Comput. Biol. - Describing the complexity of systems: multivariable set complexity and the information basis of systems biology. ( 0,703143951641299 )
J Biomed Inform - Identifying direct miRNA-mRNA causal regulatory relationships in heterogeneous data. ( 0,702526017279257 )
Comput Math Methods Med - State observer design for delayed genetic regulatory networks. ( 0,702376030041382 )
Sci Data - Transcriptomic analysis of midbrain and individual hindbrain rhombomeres in the chick embryo. ( 0,702036762924066 )
Comput Math Methods Med - Identification and functional annotation of genome-wide ER-regulated genes in breast cancer based on ChIP-Seq data. ( 0,701364258181547 )
J Biomed Inform - Prioritization of potential candidate disease genes by topological similarity of protein-protein interaction network and phenotype data. ( 0,700996251176968 )
Brief. Bioinformatics - Reconciliation of metabolites and biochemical reactions for metabolic networks. ( 0,700860653885438 )
Wiley Interdiscip Rev Syst Biol Med - Using a systems biology approach to understand and study the mechanisms of metastasis. ( 0,700746616874653 )
J Biomed Inform - Structural network analysis of biological networks for assessment of potential disease model organisms. ( 0,699507975663211 )
Comput. Biol. Med. - Revealing pathway maps of renal cell carcinoma by gene expression change. ( 0,699306998081522 )
Brief. Bioinformatics - Dissection of human MiRNA regulatory influence to subpathway. ( 0,699187986026457 )
Wiley Interdiscip Rev Syst Biol Med - Deciphering the complexities of human diseases and disorders by coupling induced-pluripotent stem cells and systems genetics. ( 0,699031807079351 )
Wiley Interdiscip Rev Syst Biol Med - Protein microarrays for genome-wide posttranslational modification analysis. ( 0,69838689947168 )