Comput Biol Chem - Prediction and verification of microRNAs related to proline accumulation under drought stress in potato.

Tópicos

{ gene(2352) biolog(1181) express(1162) }
{ import(1318) role(1303) understand(862) }
{ model(2220) cell(1177) simul(1124) }
{ use(2086) technolog(871) perceiv(783) }
{ bind(1733) structur(1185) ligand(1036) }
{ sequenc(1873) structur(1644) protein(1328) }
{ studi(2440) review(1878) systemat(933) }
{ studi(1410) differ(1259) use(1210) }
{ result(1111) use(1088) new(759) }
{ imag(2830) propos(1344) filter(1198) }
{ search(2224) databas(1162) retriev(909) }
{ perform(999) metric(946) measur(919) }
{ model(2341) predict(2261) use(1141) }
{ visual(1396) interact(850) tool(830) }
{ perform(1367) use(1326) method(1137) }
{ studi(1119) effect(1106) posit(819) }
{ model(2656) set(1616) predict(1553) }
{ decis(3086) make(1611) patient(1517) }
{ detect(2391) sensit(1101) algorithm(908) }
{ featur(3375) classif(2383) classifi(1994) }
{ problem(2511) optim(1539) algorithm(950) }
{ error(1145) method(1030) estim(1020) }
{ data(1714) softwar(1251) tool(1186) }
{ risk(3053) factor(974) diseas(938) }
{ compound(1573) activ(1297) structur(1058) }
{ first(2504) two(1366) second(1323) }
{ high(1669) rate(1365) level(1280) }
{ use(1733) differ(960) four(931) }
{ drug(1928) target(777) effect(648) }
{ implement(1333) system(1263) develop(1122) }
{ 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) }
{ method(1219) similar(1157) match(930) }
{ network(2748) neural(1063) input(814) }
{ imag(2675) segment(2577) method(1081) }
{ patient(2315) diseas(1263) diabet(1191) }
{ take(945) account(800) differ(722) }
{ motion(1329) object(1292) video(1091) }
{ assess(1506) score(1403) qualiti(1306) }
{ treatment(1704) effect(941) patient(846) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ framework(1458) process(801) describ(734) }
{ chang(1828) time(1643) increas(1301) }
{ 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) }
{ 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) }
{ featur(1941) imag(1645) propos(1176) }
{ case(1353) use(1143) diagnosi(1136) }
{ howev(809) still(633) remain(590) }
{ data(3963) clinic(1234) research(1004) }
{ research(1085) discuss(1038) issu(1018) }
{ system(1050) medic(1026) inform(1018) }
{ 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) }
{ 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) }
{ group(2977) signific(1463) compar(1072) }
{ sampl(1606) size(1419) use(1276) }
{ data(3008) multipl(1320) sourc(1022) }
{ intervent(3218) particip(2042) group(1664) }
{ activ(1138) subject(705) human(624) }
{ time(1939) patient(1703) rate(768) }
{ patient(1821) servic(1111) care(1106) }
{ can(981) present(881) function(850) }
{ analysi(2126) use(1163) compon(1037) }
{ health(1844) social(1437) communiti(874) }
{ structur(1116) can(940) graph(676) }
{ cancer(2502) breast(956) screen(824) }
{ use(976) code(926) identifi(902) }
{ survey(1388) particip(1329) question(1065) }
{ estim(2440) model(1874) function(577) }
{ process(1125) use(805) approach(778) }
{ activ(1452) weight(1219) physic(1104) }
{ method(1969) cluster(1462) data(1082) }
{ method(2212) result(1239) propos(1039) }

Resumo

Proline is an important osmotic adjusting material greatly accumulated under drought stress and can help plant to adapt to osmotic stress. MicroRNAs (miRNAs) are small, endogenous RNAs that play important regulatory roles in plant development and stress response by negatively affecting gene expression at post-transcriptional level. Three genes of pyrroline-5-carboxylate synthetase (P5CS), pyrroline-5-carboxylate reductase (P5CR) and proline dehydrogenase (ProDH) are regulating proline metabolism. Until now, little is known about miRNAs regulating proline accumulation. In this work, in order to understand whether miRNAs related to mRNAs of enzymes to regulate proline enrichment under drought stress, we used mRNAs of related enzymes as the targets of miRNAs to search miRBase using BLAST and find many query miRNA sequences. After a range of filtering criteria, 11 known miRNAs classified into 6 miRNA families were predicted. The result from qRT-PCR assay showed that 10 out of 11 predicted miRNAs were successfully detected including 9 down-regulated miRNAs and one up-regulated miRNA. Based on expression and functional analysis, we identified miR172, miR396a, miR396c and miR4233 may regulate P5CS gene, and miR2673 and miR6461 may regulate P5CR and ProDH gene, respectively. The findings can help us make a good understanding of the roles of miRNAs in regulation of proline accumulation and provide molecular evidence for involvement process of drought tolerance in potato.

Resumo Limpo

prolin import osmot adjust materi great accumul drought stress can help plant adapt osmot stress microrna mirna small endogen rnas play import regulatori role plant develop stress respons negat affect gene express posttranscript level three gene pyrrolinecarboxyl synthetas pcs pyrrolinecarboxyl reductas pcr prolin dehydrogenas prodh regul prolin metabol now littl known mirna regul prolin accumul work order understand whether mirna relat mrnas enzym regul prolin enrich drought stress use mrnas relat enzym target mirna search mirbas use blast find mani queri mirna sequenc rang filter criteria known mirna classifi mirna famili predict result qrtpcr assay show predict mirna success detect includ downregul mirna one upregul mirna base express function analysi identifi mir mira mirc mir may regul pcs gene mir mir may regul pcr prodh gene respect find can help us make good understand role mirna regul prolin accumul provid molecular evid involv process drought toler potato

Resumos Similares

J Biomed Inform - Inferring cell cycle feedback regulation from gene expression data. ( 0,887565200895644 )
Brief. Bioinformatics - Exploring the function of genetic variants in the non-coding genomic regions: approaches for identifying human regulatory variants affecting gene expression. ( 0,851069738839071 )
Comput. Biol. Med. - Genome-wide identification and structure-function studies of proteases and protease inhibitors in Cicer arietinum (chickpea). ( 0,846441732430912 )
Brief. Bioinformatics - Apoptosis regulatory protein-protein interaction demonstrates hierarchical scale-free fractal network. ( 0,8382798275853 )
Wiley Interdiscip Rev Syst Biol Med - Bioimage informatics for understanding spatiotemporal dynamics of cellular processes. ( 0,831026585437269 )
Wiley Interdiscip Rev Syst Biol Med - Establishing the stem cell state: insights from regulatory network analysis of blood stem cell development. ( 0,825894735760234 )
Comput Biol Chem - In silico identification of conserved microRNAs and their target transcripts from expressed sequence tags of three earthworm species. ( 0,807764901081896 )
Wiley Interdiscip Rev Syst Biol Med - Mathematical modeling of kidney transport. ( 0,802851624616384 )
Comput. Biol. Med. - Mathematical modeling and sensitivity analysis of the integrated TNFa-mediated apoptotic pathway for identifying key regulators. ( 0,802351082756512 )
Med Biol Eng Comput - Cell sheet integrity and nanomechanical breakdown during programmed cell death. ( 0,80231700396433 )
Wiley Interdiscip Rev Syst Biol Med - Stem cell bioengineering at the interface of systems-based models and high-throughput platforms. ( 0,801734564546871 )
Wiley Interdiscip Rev Syst Biol Med - Diverse functional networks of Tbx3 in development and disease. ( 0,800776147273832 )
Brief. Bioinformatics - Identifying miRNAs, targets and functions. ( 0,797479187121655 )
Comput. Biol. Med. - A review on the computational approaches for gene regulatory network construction. ( 0,791961219896439 )
Comput. Biol. Med. - Network-based approach reveals Y chromosome influences prostate cancer susceptibility. ( 0,791802516890178 )
Brief. Bioinformatics - Towards a comprehensive picture of the genetic landscape of complex traits. ( 0,787581476256234 )
Wiley Interdiscip Rev Syst Biol Med - Postgenomic technologies targeting the Wnt signaling network. ( 0,785889240961489 )
Brief. Bioinformatics - Transcription factor and microRNA co-regulatory loops: important regulatory motifs in biological processes and diseases. ( 0,782548038031284 )
Comput Biol Chem - Gene expression patterns combined with bioinformatics analysis identify genes associated with cholangiocarcinoma. ( 0,77958960801526 )
J Integr Bioinform - LmTDRM database: a comprehensive database on thiol metabolic gene/gene products in Listeria monocytogenes EGDe. ( 0,778349282622179 )
Wiley Interdiscip Rev Syst Biol Med - Recent advances in prostate development and links to prostatic diseases. ( 0,777443413409636 )
Med Biol Eng Comput - Vascular smooth muscle cells remodel collagen matrices by long-distance action and anisotropic interaction. ( 0,776611889188001 )
J Integr Bioinform - A study of the short and long-term regulation of E. coli metabolic pathways. ( 0,776138535527371 )
Brief. Bioinformatics - Evolution of gene regulation--on the road towards computational inferences. ( 0,7756499573484 )
Wiley Interdiscip Rev Syst Biol Med - Cardiac function and disease: emerging role of small ubiquitin-related modifier. ( 0,774354522148758 )
Wiley Interdiscip Rev Syst Biol Med - Genome-wide approaches in the study of microRNA biology. ( 0,770912478704336 )
Wiley Interdiscip Rev Syst Biol Med - Sex and the circuitry: progress toward a systems-level understanding of vertebrate sex determination. ( 0,770826157797153 )
J Biomed Inform - The detection of risk pathways, regulated by miRNAs, via the integration of sample-matched miRNA-mRNA profiles and pathway structure. ( 0,769952421814093 )
J Am Med Inform Assoc - Extracting coordinated patterns of DNA methylation and gene expression in ovarian cancer. ( 0,765562998241603 )
Sci Data - DNA methylation temporal profiling following peripheral versus central nervous system axotomy. ( 0,764325593431524 )
J Integr Bioinform - miReg: a resource for microRNA regulation. ( 0,764321687977206 )
Comput. Biol. Med. - Revealing pathway maps of renal cell carcinoma by gene expression change. ( 0,76138732725758 )
Wiley Interdiscip Rev Syst Biol Med - miRNA regulation in the context of functional protein networks: principles and applications. ( 0,759371700068767 )
J Integr Bioinform - Network expansion and pathway enrichment analysis towards biologically significant findings from microarrays. ( 0,759262348115387 )
Comput Math Methods Med - Systematic analysis of time-series gene expression data on tumor cell-selective apoptotic responses to HDAC inhibitors. ( 0,752271614996391 )
Comput Biol Chem - Detecting adaptive evolution and functional divergence in aminocyclopropane-1-carboxylate synthase (ACS) gene family. ( 0,751655071298658 )
Comput Math Methods Med - Integrating gene expression and protein interaction data for signaling pathway prediction of Alzheimer's disease. ( 0,750515881080833 )
Comput Biol Chem - Identification of novel splice variants and exons of human endothelial cell-specific chemotaxic regulator (ECSCR) by bioinformatics analysis. ( 0,749867216852839 )
Comput Biol Chem - Disruption of murine Tcte3-3 induces tissue specific apoptosis via co-expression of Anxa5 and Pebp1. ( 0,747191400492156 )
Brief. Bioinformatics - Revealing the architecture of genetic and epigenetic regulation: a maximum likelihood model. ( 0,744526649331937 )
Comput Math Methods Med - Understanding the pathogenesis of Kawasaki disease by network and pathway analysis. ( 0,742713093827078 )
Comput Biol Chem - Large-scale mining co-expressed genes in Arabidopsis anther: from pair to group. ( 0,740502204832087 )
Wiley Interdiscip Rev Syst Biol Med - Understanding multimodal biological decisions from single cell and population dynamics. ( 0,7404028737035 )
J Am Med Inform Assoc - Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseases. ( 0,738437650485932 )
Comput. Biol. Med. - Identification and analysis of the regulatory network of Myc and microRNAs from high-throughput experimental data. ( 0,735841921692676 )
J. Comput. Biol. - Vavien: an algorithm for prioritizing candidate disease genes based on topological similarity of proteins in interaction networks. ( 0,735811037308869 )
Comput Math Methods Med - First comprehensive in silico analysis of the functional and structural consequences of SNPs in human GalNAc-T1 gene. ( 0,735782769285489 )
J Biomed Inform - Structural network analysis of biological networks for assessment of potential disease model organisms. ( 0,735478582412972 )
J Integr Bioinform - Computer and statistical analysis of transcription factor binding and chromatin modifications by ChIP-seq data in embryonic stem cell. ( 0,735405192685999 )
J. Comput. Biol. - Bioinformatics method to analyze the mechanism of pancreatic cancer disorder. ( 0,733005624921805 )
Wiley Interdiscip Rev Syst Biol Med - The adaptor protein LAT serves as an integration node for signaling pathways that drive T cell activation. ( 0,732010476887187 )
J. Comput. Biol. - Stochastic simulation of notch signaling reveals novel factors that mediate the differentiation of neural stem cells. ( 0,731967036368287 )
Comput Biol Chem - Bioinformatic analysis of molecular network of glucosinolate biosynthesis. ( 0,72978069926602 )
Comput Math Methods Med - Dynamic regulatory network reconstruction for Alzheimer's disease based on matrix decomposition techniques. ( 0,7280354890623 )
Wiley Interdiscip Rev Syst Biol Med - Systems biology of adipose tissue metabolism: regulation of growth, signaling and inflammation. ( 0,726361219909422 )
Comput Biol Chem - Identification of miR159s and their target genes and expression analysis under drought stress in potato. ( 0,725853476611095 )
Artif Intell Med - Identifying regulatory relationships among genomic loci, biological pathways, and disease. ( 0,723845627659418 )
Comput. Biol. Med. - Degrees of separation as a statistical tool for evaluating candidate genes. ( 0,723334535272952 )
Wiley Interdiscip Rev Syst Biol Med - Protein microarrays for genome-wide posttranslational modification analysis. ( 0,721470675591378 )
Wiley Interdiscip Rev Syst Biol Med - Where gene discovery turns into systems biology: genome-scale RNAi screens in Drosophila. ( 0,719259697435986 )
J Integr Bioinform - BacillusRegNet: a transcriptional regulation database and analysis platform for Bacillus species. ( 0,718985260350533 )
Wiley Interdiscip Rev Syst Biol Med - Reverse-engineering human regulatory networks. ( 0,718761451703756 )
Comput Biol Chem - Statistical analysis of combinatorial transcriptional regulatory motifs in human intron-containing promoter sequences. ( 0,71829501279229 )
Wiley Interdiscip Rev Syst Biol Med - Role of fibroblast growth factor signaling in vascular formation and maintenance: orchestrating signaling networks as an integrated system. ( 0,717285304524386 )
J Integr Bioinform - An integrative bioinformatics framework for genome-scale multiple level network reconstruction of rice. ( 0,716668246701941 )
Wiley Interdiscip Rev Syst Biol Med - Using a systems biology approach to understand and study the mechanisms of metastasis. ( 0,71476813127992 )
Comput Biol Chem - lncRNAMap: a map of putative regulatory functions in the long non-coding transcriptome. ( 0,714760451680219 )
J Integr Bioinform - Predicting breast cancer chemotherapeutic response using a novel tool for microarray data analysis. ( 0,714088553869038 )
J Biomed Inform - Autism candidate genes via mouse phenomics. ( 0,713639570879971 )
Brief. Bioinformatics - Toward the dynamic interactome: it's about time. ( 0,712658622552537 )
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. ( 0,712320185778444 )
Comput Math Methods Med - Identification and functional annotation of genome-wide ER-regulated genes in breast cancer based on ChIP-Seq data. ( 0,71215124105762 )
J Am Med Inform Assoc - Identifying disease genes and module biomarkers by differential interactions. ( 0,711548148370199 )
Wiley Interdiscip Rev Syst Biol Med - Regulatory variation: an emerging vantage point for cancer biology. ( 0,70989711251779 )
J Integr Bioinform - Community structure of non-coding RNA interaction network. ( 0,707721007645343 )
J Biomed Inform - Gene pathways and subnetworks distinguish between major glioma subtypes and elucidate potential underlying biology. ( 0,70634325327852 )
Wiley Interdiscip Rev Syst Biol Med - Toward a quantitative understanding of the Wnt/?-catenin pathway through simulation and experiment. ( 0,705906740248019 )
Wiley Interdiscip Rev Syst Biol Med - Using variability in gene expression as a tool for studying gene regulation. ( 0,705468846993621 )
J Biomed Inform - A comparative study of covariance selection models for the inference of gene regulatory networks. ( 0,705305591895022 )
Sci Data - miRNA expression atlas in male rat. ( 0,705260347927233 )
Wiley Interdiscip Rev Syst Biol Med - Signaling networks in palate development. ( 0,705214763995519 )
Wiley Interdiscip Rev Syst Biol Med - Engineered genetic information processing circuits. ( 0,704854388507508 )
J Biomed Inform - Data driven linear algebraic methods for analysis of molecular pathways: application to disease progression in shock/trauma. ( 0,704762243851983 )
Artif Intell Med - Integration of gene signatures using biological knowledge. ( 0,704646727838719 )
Artif Intell Med - An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods. ( 0,702150969635954 )
J Integr Bioinform - Assembling cell context-specific gene sets: a case in cardiomyopathy. ( 0,701334778341419 )
J Integr Bioinform - Towards prediction and prioritization of disease genes by the modularity of human phenome-genome assembled network. ( 0,70124247935181 )
Brief. Bioinformatics - Causes, consequences and solutions of phylogenetic incongruence. ( 0,700985719812273 )
J Integr Bioinform - Applying the tuple space-based approach to the simulation of the caspases, an essential signalling pathway. ( 0,700043084770787 )
Wiley Interdiscip Rev Syst Biol Med - Cyclic nucleotide signaling in intestinal epithelia: getting to the gut of the matter. ( 0,699670991865232 )
J Am Med Inform Assoc - Knowledge boosting: a graph-based integration approach with multi-omics data and genomic knowledge for cancer clinical outcome prediction. ( 0,698748072421017 )
AMIA Annu Symp Proc - Towards mechanism classifiers: expression-anchored Gene Ontology signature predicts clinical outcome in lung adenocarcinoma patients. ( 0,698201346404605 )
Comput. Biol. Med. - Prediction of microRNA-regulated protein interaction pathways in Arabidopsis using machine learning algorithms. ( 0,697598766236984 )
J Chem Inf Model - Molecular dynamics simulations reveal a novel mechanism for ATP inhibition of insulin degrading enzyme. ( 0,695965717556947 )
J Am Med Inform Assoc - An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer. ( 0,695081275363125 )
Wiley Interdiscip Rev Syst Biol Med - Noncoding RNAs in gene regulation. ( 0,692513429688841 )
J Chem Inf Model - Scoring function based approach for locating binding sites and understanding recognition mechanism of protein-DNA complexes. ( 0,691676511577789 )
Wiley Interdiscip Rev Syst Biol Med - Mediators and dynamics of DNA methylation. ( 0,691605981777235 )
Brief. Bioinformatics - How to cluster gene expression dynamics in response to environmental signals. ( 0,691415473630405 )
Brief. Bioinformatics - Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication. ( 0,690267745790171 )