{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T22:03:41Z","timestamp":1762898621923},"reference-count":39,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2010,7,1]],"date-time":"2010-07-01T00:00:00Z","timestamp":1277942400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1000843","type":"journal-article","created":{"date-parts":[[2010,7,1]],"date-time":"2010-07-01T21:02:29Z","timestamp":1278018149000},"page":"e1000843","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":47,"title":["Intergenic and Repeat Transcription in Human, Chimpanzee and Macaque Brains Measured by RNA-Seq"],"prefix":"10.1371","volume":"6","author":[{"given":"Augix","family":"Guohua Xu","sequence":"first","affiliation":[]},{"given":"Liu","family":"He","sequence":"additional","affiliation":[]},{"given":"Zhongshan","family":"Li","sequence":"additional","affiliation":[]},{"given":"Ying","family":"Xu","sequence":"additional","affiliation":[]},{"given":"Mingfeng","family":"Li","sequence":"additional","affiliation":[]},{"given":"Xing","family":"Fu","sequence":"additional","affiliation":[]},{"given":"Zheng","family":"Yan","sequence":"additional","affiliation":[]},{"given":"Yuan","family":"Yuan","sequence":"additional","affiliation":[]},{"given":"Corinna","family":"Menzel","sequence":"additional","affiliation":[]},{"given":"Na","family":"Li","sequence":"additional","affiliation":[]},{"given":"Mehmet","family":"Somel","sequence":"additional","affiliation":[]},{"given":"Hao","family":"Hu","sequence":"additional","affiliation":[]},{"given":"Wei","family":"Chen","sequence":"additional","affiliation":[]},{"given":"Svante","family":"P\u00e4\u00e4bo","sequence":"additional","affiliation":[]},{"given":"Philipp","family":"Khaitovich","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2010,7,1]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"424","DOI":"10.1093\/bfgp\/elp037","article-title":"Establishing legitimacy and function in the new transcriptome.","volume":"8","author":"H van Bakel","year":"2009","journal-title":"Brief Funct Genomic Proteomic"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/nrg2521","article-title":"Long non-coding RNAs: insights into functions.","volume":"10","author":"TR Mercer","year":"2009","journal-title":"Nat Rev Genet"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"R74","DOI":"10.1186\/gb-2004-5-10-r74","article-title":"Variation in alternative splicing across human tissues.","volume":"5","author":"G Yeo","year":"2004","journal-title":"Genome Biol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"1413","DOI":"10.1038\/ng.259","article-title":"Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing.","volume":"40","author":"Q Pan","year":"2008","journal-title":"Nat Genet"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1126\/science.1090005","article-title":"Evolution at two levels in humans and chimpanzees.","volume":"188","author":"MC King","year":"1975","journal-title":"Science"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1126\/science.1068996","article-title":"Intra- and interspecific variation in primate gene expression patterns.","volume":"296","author":"W Enard","year":"2002","journal-title":"Science"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"13030","DOI":"10.1073\/pnas.2135499100","article-title":"Elevated gene expression levels distinguish human from non-human primate brains.","volume":"100","author":"M C\u00e1ceres","year":"2003","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1016\/S0168-9525(02)00040-9","article-title":"Induced gene expression in human brain after the split from chimpanzee.","volume":"19","author":"J Gu","year":"2003","journal-title":"Trends Genet"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"e171","DOI":"10.1371\/journal.pgen.0020171","article-title":"Functionality of intergenic transcription: an evolutionary comparison.","volume":"2","author":"P Khaitovich","year":"2006","journal-title":"PLoS Genet"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/nmeth.1226","article-title":"Mapping and quantifying mammalian transcriptomes by RNA-Seq.","volume":"5","author":"A Mortazavi","year":"2008","journal-title":"Nat Methods"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"81","DOI":"10.2144\/000112900","article-title":"Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing.","volume":"45","author":"R Morin","year":"2008","journal-title":"Biotechniques"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"e2803","DOI":"10.1371\/journal.pone.0002803","article-title":"Poly A- transcripts expressed in HeLa cells.","volume":"3","author":"Q Wu","year":"2008","journal-title":"PLoS One"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1038\/ng.368","article-title":"The regulated retrotransposon transcriptome of mammalian cells.","volume":"41","author":"GJ Faulkner","year":"2009","journal-title":"Nat Genet"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"1034","DOI":"10.1101\/gr.3715005","article-title":"Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.","volume":"15","author":"A Siepel","year":"2005","journal-title":"Genome Research"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.","volume":"25","author":"M Ashburner","year":"2000","journal-title":"Nat Genet"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: kyoto encyclopedia of genes and genomes.","volume":"28","author":"M Kanehisa","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"1823","DOI":"10.1101\/gr.6679507","article-title":"Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.","volume":"17","author":"MF Lin","year":"2007","journal-title":"Genome Research"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1038\/nature07672","article-title":"Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals.","volume":"458","author":"M Guttman","year":"2009","journal-title":"Nature"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"11667","DOI":"10.1073\/pnas.0904715106","article-title":"Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression.","volume":"106","author":"AM Khalil","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"e33","DOI":"10.1371\/journal.pcbi.0020033","article-title":"Identification and classification of conserved RNA secondary structures in the human genome.","volume":"2","author":"JS Pedersen","year":"2006","journal-title":"PLoS Comput Biol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.","volume":"26","author":"MD Robinson","journal-title":"Bioinformatics"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"1462","DOI":"10.1101\/gr.2538704","article-title":"Regional patterns of gene expression in human and chimpanzee brains.","volume":"14","author":"P Khaitovich","year":"2004","journal-title":"Genome Research"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"22358","DOI":"10.1073\/pnas.0911376106","article-title":"Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain.","volume":"106","author":"K Nowick","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"1140","DOI":"10.1038\/ng2104","article-title":"Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution.","volume":"39","author":"R Haygood","year":"2007","journal-title":"Nat Genet"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1038\/nature04559","article-title":"Expression profiling in primates reveals a rapid evolution of human transcription factors.","volume":"440","author":"Y Gilad","year":"2006","journal-title":"Nature"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"e3625","DOI":"10.1371\/journal.pone.0003625","article-title":"Genomic convergence analysis of schizophrenia: mRNA sequencing reveals altered synaptic vesicular transport in post-mortem cerebellum.","volume":"3","author":"J Mudge","year":"2008","journal-title":"PLoS One"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1038\/nature08170","article-title":"Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps.","volume":"460","author":"SW Chi","year":"2009","journal-title":"Nature"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"1643","DOI":"10.1126\/science.1155390","article-title":"Proliferating cells express mRNAs with shortened 3\u2032 untranslated regions and fewer microRNA target sites.","volume":"320","author":"R Sandberg","year":"2008","journal-title":"Science"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"7028","DOI":"10.1073\/pnas.0900028106","article-title":"Progressive lengthening of 3\u2032 untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development.","volume":"106","author":"Z Ji","year":"2009","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1093\/bioinformatics\/btn025","article-title":"SOAP: short oligonucleotide alignment program.","volume":"24","author":"R Li","year":"2008","journal-title":"Bioinformatics"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1093\/nar\/30.1.38","article-title":"The Ensembl genome database project.","volume":"30","author":"T Hubbard","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"D493","DOI":"10.1093\/nar\/gkh103","article-title":"The UCSC Table Browser data retrieval tool.","volume":"32","author":"D Karolchik","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1101\/gr.1933104","article-title":"Aligning multiple genomic sequences with the threaded blockset aligner.","volume":"14","author":"M Blanchette","year":"2004","journal-title":"Genome Res"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"D773","DOI":"10.1093\/nar\/gkm966","article-title":"The UCSC Genome Browser Database: 2008 update.","volume":"36","author":"D Karolchik","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1093\/bioinformatics\/19.2.185","article-title":"A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.","volume":"19","author":"BM Bolstad","year":"2003","journal-title":"Bioinformatics"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1186\/1471-2105-8-41","article-title":"FUNC: a package for detecting significant associations between gene sets and ontological annotations.","volume":"8","author":"K Prufer","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1038\/nature04072","article-title":"Initial sequence of the chimpanzee genome and comparison with the human genome.","volume":"437","year":"2005","journal-title":"Nature"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"1850","DOI":"10.1126\/science.1108296","article-title":"Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees.","volume":"309","author":"P Khaitovich","year":"2005","journal-title":"Science"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"e137","DOI":"10.1371\/journal.pcbi.0030137","article-title":"Evolutionary history of mammalian transposons determined by genome-wide defragmentation.","volume":"3","author":"J Giordano","year":"2007","journal-title":"PLoS Comput Biol"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000843","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,30]],"date-time":"2019-05-30T17:12:21Z","timestamp":1559236341000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000843"}},"subtitle":[],"editor":[{"given":"Adam","family":"Siepel","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2010,7,1]]},"references-count":39,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2010,7,1]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000843","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,7,1]]}}}