J. Comput. Biol. - AREM: aligning short reads from ChIP-sequencing by expectation maximization.

Tópicos

{ sequenc(1873) structur(1644) protein(1328) }
{ gene(2352) biolog(1181) express(1162) }
{ spatial(1525) area(1432) region(1030) }
{ use(2086) technolog(871) perceiv(783) }
{ import(1318) role(1303) understand(862) }
{ signal(2180) analysi(812) frequenc(800) }
{ model(3404) distribut(989) bayesian(671) }
{ algorithm(1844) comput(1787) effici(935) }
{ search(2224) databas(1162) retriev(909) }
{ bind(1733) structur(1185) ligand(1036) }
{ implement(1333) system(1263) develop(1122) }
{ estim(2440) model(1874) function(577) }
{ perform(1367) use(1326) method(1137) }
{ data(2317) use(1299) case(1017) }
{ can(981) present(881) function(850) }
{ data(1737) use(1416) pattern(1282) }
{ imag(2830) propos(1344) filter(1198) }
{ error(1145) method(1030) estim(1020) }
{ clinic(1479) use(1117) guidelin(835) }
{ model(2341) predict(2261) use(1141) }
{ state(1844) use(1261) util(961) }
{ model(2656) set(1616) predict(1553) }
{ first(2504) two(1366) second(1323) }
{ use(976) code(926) identifi(902) }
{ method(1219) similar(1157) match(930) }
{ motion(1329) object(1292) video(1091) }
{ assess(1506) score(1403) qualiti(1306) }
{ data(1714) softwar(1251) tool(1186) }
{ general(901) number(790) one(736) }
{ data(3008) multipl(1320) sourc(1022) }
{ patient(1821) servic(1111) care(1106) }
{ analysi(2126) use(1163) compon(1037) }
{ high(1669) rate(1365) level(1280) }
{ method(1969) cluster(1462) data(1082) }
{ can(774) often(719) complex(702) }
{ imag(1947) propos(1133) code(1026) }
{ inform(2794) health(2639) internet(1427) }
{ system(1976) rule(880) can(841) }
{ measur(2081) correl(1212) valu(896) }
{ imag(1057) registr(996) error(939) }
{ featur(3375) classif(2383) classifi(1994) }
{ network(2748) neural(1063) input(814) }
{ imag(2675) segment(2577) method(1081) }
{ patient(2315) diseas(1263) diabet(1191) }
{ take(945) account(800) differ(722) }
{ studi(2440) review(1878) systemat(933) }
{ treatment(1704) effect(941) patient(846) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ framework(1458) process(801) describ(734) }
{ problem(2511) optim(1539) algorithm(950) }
{ chang(1828) time(1643) increas(1301) }
{ learn(2355) train(1041) set(1003) }
{ concept(1167) ontolog(924) domain(897) }
{ 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) }
{ care(1570) inform(1187) nurs(1089) }
{ 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) }
{ 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) }
{ visual(1396) interact(850) tool(830) }
{ compound(1573) activ(1297) structur(1058) }
{ studi(1119) effect(1106) posit(819) }
{ blood(1257) pressur(1144) flow(957) }
{ 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) }
{ cost(1906) reduc(1198) effect(832) }
{ group(2977) signific(1463) compar(1072) }
{ sampl(1606) size(1419) use(1276) }
{ intervent(3218) particip(2042) group(1664) }
{ activ(1138) subject(705) human(624) }
{ time(1939) patient(1703) rate(768) }
{ health(1844) social(1437) communiti(874) }
{ structur(1116) can(940) graph(676) }
{ cancer(2502) breast(956) screen(824) }
{ use(1733) differ(960) four(931) }
{ drug(1928) target(777) effect(648) }
{ result(1111) use(1088) new(759) }
{ survey(1388) particip(1329) question(1065) }
{ decis(3086) make(1611) patient(1517) }
{ process(1125) use(805) approach(778) }
{ activ(1452) weight(1219) physic(1104) }
{ method(2212) result(1239) propos(1039) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

High-throughput sequencing coupled to chromatin immunoprecipitation (ChIP-Seq) is widely used in characterizing genome-wide binding patterns of transcription factors, cofactors, chromatin modifiers, and other DNA binding proteins. A key step in ChIP-Seq data analysis is to map short reads from high-throughput sequencing to a reference genome and identify peak regions enriched with short reads. Although several methods have been proposed for ChIP-Seq analysis, most existing methods only consider reads that can be uniquely placed in the reference genome, and therefore have low power for detecting peaks located within repeat sequences. Here, we introduce a probabilistic approach for ChIP-Seq data analysis that utilizes all reads, providing a truly genome-wide view of binding patterns. Reads are modeled using a mixture model corresponding to K enriched regions and a null genomic background. We use maximum likelihood to estimate the locations of the enriched regions, and implement an expectation-maximization (E-M) algorithm, called AREM (aligning reads by expectation maximization), to update the alignment probabilities of each read to different genomic locations. We apply the algorithm to identify genome-wide binding events of two proteins: Rad21, a component of cohesin and a key factor involved in chromatid cohesion, and Srebp-1, a transcription factor important for lipid/cholesterol homeostasis. Using AREM, we were able to identify 19,935 Rad21 peaks and 1,748 Srebp-1 peaks in the mouse genome with high confidence, including 1,517 (7.6%) Rad21 peaks and 227 (13%) Srebp-1 peaks that were missed using only uniquely mapped reads. The open source implementation of our algorithm is available at http://sourceforge.net/projects/arem.

Resumo Limpo

highthroughput sequenc coupl chromatin immunoprecipit chipseq wide use character genomewid bind pattern transcript factor cofactor chromatin modifi dna bind protein key step chipseq data analysi map short read highthroughput sequenc refer genom identifi peak region enrich short read although sever method propos chipseq analysi exist method consid read can uniqu place refer genom therefor low power detect peak locat within repeat sequenc introduc probabilist approach chipseq data analysi util read provid truli genomewid view bind pattern read model use mixtur model correspond k enrich region null genom background use maximum likelihood estim locat enrich region implement expectationmaxim em algorithm call arem align read expect maxim updat align probabl read differ genom locat appli algorithm identifi genomewid bind event two protein rad compon cohesin key factor involv chromatid cohes srebp transcript factor import lipidcholesterol homeostasi use arem abl identifi rad peak srebp peak mous genom high confid includ rad peak srebp peak miss use uniqu map read open sourc implement algorithm avail httpsourceforgenetprojectsarem

Resumos Similares

J Chem Inf Model - Modules identification in protein structures: the topological and geometrical solutions. ( 0,802436082174134 )
Comput Biol Chem - In silico characterization and evolutionary analyses of CCAAT binding proteins in the lycophyte plant Selaginella moellendorffii genome: a growing comparative genomics resource. ( 0,783801046370393 )
Comput Biol Chem - Identification of putative and potential cross-reactive chickpea (Cicer arietinum) allergens through an in silico approach. ( 0,781218400874795 )
Comput Biol Chem - Human-chimpanzee alignment: ortholog exponentials and paralog power laws. ( 0,779010325476478 )
Comput Biol Chem - ProSTRIP: A method to find similar structural repeats in three-dimensional protein structures. ( 0,772857956179213 )
J. Comput. Biol. - Nonparametric combinatorial sequence models. ( 0,766198849972366 )
J Chem Inf Model - ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures. ( 0,765304955282901 )
Brief. Bioinformatics - New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. ( 0,765033747398996 )
Comput. Biol. Med. - An insight into the molecular basis for convergent evolution in fish antifreeze Proteins. ( 0,762501048655731 )
Comput Biol Chem - Analysis of sequence repeats of proteins in the PDB. ( 0,75804531515258 )
Comput Biol Chem - Computational insight into nitration of human myoglobin. ( 0,754514818211131 )
Comput Biol Chem - The frequency of poly(G) tracts in the human genome and their use as a sensor of DNA damage. ( 0,752548979356139 )
Comput Biol Chem - Multi-nucleation and vectorial folding pathways of large helix protein. ( 0,752042081350269 )
Comput Biol Chem - Characterizing regions in the human genome unmappable by next-generation-sequencing at the read length of 1000 bases. ( 0,750951085986005 )
Brief. Bioinformatics - Sequencing technologies and tools for short tandem repeat variation detection. ( 0,749223872146751 )
BMC Med Inform Decis Mak - Efficient protein structure search using indexing methods. ( 0,745836180886199 )
Brief. Bioinformatics - Systematic identification of Class I HDAC substrates. ( 0,74322438320217 )
Comput Biol Chem - Bacterial protein structures reveal phylum dependent divergence. ( 0,741361845512043 )
Brief. Bioinformatics - Applications of alignment-free methods in epigenomics. ( 0,736415336001754 )
Brief. Bioinformatics - De novo assembly of short sequence reads. ( 0,735178370891019 )
J. Comput. Biol. - Simultaneous alignment and folding of protein sequences. ( 0,73446429693398 )
Comput Biol Chem - Identical sequence patterns in the ends of exons and introns of human protein-coding genes. ( 0,734060966739799 )
Comput Biol Chem - The challenge of annotating protein sequences: The tale of eight domains of unknown function in Pfam. ( 0,731575809010507 )
Comput Biol Chem - Large replication skew domains delimit GC-poor gene deserts in human. ( 0,730711986175686 )
Comput Biol Chem - ProCoCoA: A quantitative approach for analyzing protein core composition. ( 0,72943784142458 )
J Chem Inf Model - Tertiary structure prediction of RNA-RNA complexes using a secondary structure and fragment-based method. ( 0,728604280478 )
J Chem Inf Model - Protein secondary structure prediction with SPARROW. ( 0,727915846990624 )
Comput Biol Chem - Statistical analysis and exposure status classification of transmembrane beta barrel residues. ( 0,727352495021155 )
J Chem Inf Model - Parallel and antiparallel ?-strands differ in amino acid composition and availability of short constituent sequences. ( 0,7268800433079 )
Comput Biol Chem - Gene expression regulation of the PF00480 or PF14340 domain proteins suggests their involvement in sulfur metabolism. ( 0,725903219355699 )
Sci Data - Comprehensive analysis of the venom gland transcriptome of the spider Dolomedes fimbriatus. ( 0,725882858326237 )
Comput. Biol. Med. - Improving protein complex classification accuracy using amino acid composition profile. ( 0,725683325447756 )
Comput Biol Chem - Gene cloning, homology comparison and analysis of the main functional structure domains of beta estrogen receptor in Jining Gray goat. ( 0,725343128332468 )
Sci Data - Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus. ( 0,721056396774715 )
J. Comput. Biol. - Evaluating, comparing, and interpreting protein domain hierarchies. ( 0,720897576650475 )
Comput Biol Chem - Identification of potential drug targets by subtractive genome analysis of Bacillus anthracis A0248: An in silico approach. ( 0,720603966423744 )
J. Comput. Biol. - Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis. ( 0,72028067792267 )
Comput Biol Chem - Genome-wide analysis and evolutionary study of sucrose non-fermenting 1-related protein kinase 2 (SnRK2) gene family members in Arabidopsis and Oryza. ( 0,71970966416485 )
Comput Biol Chem - Protein fold recognition based on functional domain composition. ( 0,718695590143275 )
J. Comput. Biol. - ComB: SNP calling and mapping analysis for color and nucleotide space platforms. ( 0,718408416266746 )
Curr Protoc Bioinformatics - Using the RNAstructure Software Package to Predict Conserved RNA Structures. ( 0,717611966229881 )
J. Comput. Biol. - Combinatorics of -structures. ( 0,716384069775674 )
Comput. Biol. Med. - A content and structural assessment of oxidative motifs across a diverse set of life forms. ( 0,715784643301318 )
Brief. Bioinformatics - Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. ( 0,715652585595647 )
J Integr Bioinform - Exceptional single strand DNA word symmetry: analysis of evolutionary potentialities. ( 0,715597661051204 )
J Chem Inf Model - Comparative analysis of threshold and tessellation methods for determining protein contacts. ( 0,713541959885772 )
Comput Biol Chem - A novel empirical mutual information approach to identify co-evolving amino acid positions of influenza A viruses. ( 0,712054141636237 )
J Integr Bioinform - Predicting protein distance maps according to physicochemical properties. ( 0,711284747806051 )
J Integr Bioinform - Prediction of thioredoxin and glutaredoxin target proteins by identifying reversibly oxidized cysteinyl residues. ( 0,708063325404052 )
Comput Biol Chem - Predicting protein-RNA interaction amino acids using random forest based on submodularity subset selection. ( 0,706732892155374 )
J. Comput. Biol. - Statistical significance of threading scores. ( 0,706697015714978 )
Comput. Biol. Med. - Improving protein secondary structure prediction using a multi-modal BP method. ( 0,706631421355438 )
J Chem Inf Model - Protein structural statistics with PSS. ( 0,70534792486485 )
J. Comput. Biol. - Reconstructing the history of large-scale genomic changes: biological questions and computational challenges. ( 0,70354285691928 )
Comput Biol Chem - Global expression analysis of miRNA gene cluster and family based on isomiRs from deep sequencing data. ( 0,702744195963592 )
J. Comput. Biol. - Sequence alignment of viral channel proteins with cellular ion channels. ( 0,698620528412363 )
J. Comput. Biol. - Using structural and evolutionary information to detect and correct pyrosequencing errors in noncoding RNAs. ( 0,697191472528952 )
J. Comput. Biol. - IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information. ( 0,696926673706385 )
Comput Biol Chem - A local average connectivity-based method for identifying essential proteins from the network level. ( 0,694335161281802 )
Brief. Bioinformatics - Ortholog identification in the presence of domain architecture rearrangement. ( 0,69416918643765 )
Comput Methods Programs Biomed - Pinda: a web service for detection and analysis of intraspecies gene duplication events. ( 0,693757041823472 )
J Chem Inf Model - Improved helix and kink characterization in membrane proteins allows evaluation of kink sequence predictors. ( 0,693731695586411 )
BMC Med Inform Decis Mak - Improved method for protein complex detection using bottleneck proteins. ( 0,69370688458676 )
Comput. Biol. Med. - miRClassify: an advanced web server for miRNA family classification and annotation. ( 0,691358165110805 )
Comput Biol Chem - Analysis of the relationships between evolvability, thermodynamics, and the functions of intrinsically disordered proteins/regions. ( 0,691235162824588 )
Comput Math Methods Med - DV-curve representation of protein sequences and its application. ( 0,68906164546461 )
J Chem Inf Model - Protein secondary structure classification revisited: processing DSSP information with PSSC. ( 0,687806932586275 )
Brief. Bioinformatics - Application of second-generation sequencing to cancer genomics. ( 0,687166012968265 )
Brief. Bioinformatics - Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. ( 0,686190453751946 )
Brief. Bioinformatics - A practical guide for the computational selection of residues to be experimentally characterized in protein families. ( 0,685706177118229 )
Brief. Bioinformatics - Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes). ( 0,684382005571141 )
J. Comput. Biol. - Efficient traversal of beta-sheet protein folding pathways using ensemble models. ( 0,68377879638658 )
J. Comput. Biol. - Learning cellular sorting pathways using protein interactions and sequence motifs. ( 0,681901332600616 )
J. Comput. Biol. - Statistical significance of optical map alignments. ( 0,681696685205771 )
Comput Biol Chem - Identification and characterization of lysine-methylated sites on histones and non-histone proteins. ( 0,680422496714749 )
Comput Biol Chem - Analysis of compensatory substitution and gene evolution on the MAGEA/CSAG-palindrome of the primate X chromosomes. ( 0,678370338194317 )
Comput Math Methods Med - Uses of phage display in agriculture: sequence analysis and comparative modeling of late embryogenesis abundant client proteins suggest protein-nucleic acid binding functionality. ( 0,677696387005521 )
J Chem Inf Model - Building a knowledge-based statistical potential by capturing high-order inter-residue interactions and its applications in protein secondary structure assessment. ( 0,676087062496118 )
Comput Biol Chem - Molecular phylogenetic study and expression analysis of ATP-binding cassette transporter gene family in Oryza sativa in response to salt stress. ( 0,676008668318714 )
Comput Biol Chem - Systematic analysis of an amidase domain CHAP in 12 Staphylococcus aureus genomes and 44 staphylococcal phage genomes. ( 0,67391230708779 )
J. Comput. Biol. - A probabilistic model of neutral and selective dynamics of protein network evolution. ( 0,673682733768834 )
J. Comput. Biol. - CNVeM: copy number variation detection using uncertainty of read mapping. ( 0,673602155530347 )
Comput Biol Chem - Computational determination of the orientation of a heat repeat-like domain of DNA-PKcs. ( 0,671436979724232 )
J Chem Inf Model - Kink characterization and modeling in transmembrane protein structures. ( 0,669915632933779 )
Med Biol Eng Comput - Ataxin active site determination using spectral distribution of electron ion interaction potentials of amino acids. ( 0,669162785100919 )
Sci Data - Long-read, whole-genome shotgun sequence data for five model organisms. ( 0,667725521478996 )
Curr Protoc Bioinformatics - An Overview of RNA Sequence Analyses: Structure Prediction, ncRNA Gene Identification, and RNAi Design. ( 0,666527958690873 )
Comput Biol Chem - Semantically predicting protein functions based on protein functional connectivity. ( 0,665748117681406 )
Med Biol Eng Comput - The influence of alignment-free sequence representations on the semi-supervised classification of class C G protein-coupled receptors: semi-supervised classification of class C GPCRs. ( 0,665141965352668 )
Comput. Biol. Med. - The possible role of HSPs on Beh?et's disease: a bioinformatic approach. ( 0,664841391060224 )
Comput Biol Chem - Relationship between global structural parameters and Enzyme Commission hierarchy: implications for function prediction. ( 0,664214776540768 )
Comput. Biol. Med. - New layers in understanding and predicting a-linolenic acid content in plants using amino acid characteristics of omega-3 fatty acid desaturase. ( 0,6641414880008 )
J. Comput. Biol. - LB3D: a protein three-dimensional substructure search program based on the lower bound of a root mean square deviation value. ( 0,662980352048627 )
Comput Math Methods Med - Quad-PRE: a hybrid method to predict protein quaternary structure attributes. ( 0,661977707387066 )
Brief. Bioinformatics - Identify drug repurposing candidates by mining the protein data bank. ( 0,661212254945819 )
J Integr Bioinform - LmTDRM database: a comprehensive database on thiol metabolic gene/gene products in Listeria monocytogenes EGDe. ( 0,660971309853077 )
Med Biol Eng Comput - Enhanced spatio-temporal alignment of plantar pressure image sequences using B-splines. ( 0,660259140714587 )
J Integr Bioinform - BacillusRegNet: a transcriptional regulation database and analysis platform for Bacillus species. ( 0,659810833281656 )
Comput. Biol. Med. - Application of 2D graphic representation of protein sequence based on Huffman tree method. ( 0,659007069439502 )
Comput Biol Chem - Genes under positive selection in Mycobacterium tuberculosis. ( 0,658396476583302 )