{"id":"https://openalex.org/W207474797","doi":null,"title":"Expression and chromatin association of noncoding RNAs","display_name":"Expression and chromatin association of noncoding RNAs","publication_year":2011,"publication_date":"2011-08-01","ids":{"openalex":"https://openalex.org/W207474797","mag":"207474797"},"language":"en","primary_location":{"id":"mag:207474797","doi":null,"is_oa":false,"landing_page_url":"https://espace.library.uq.edu.au/view/UQ:262118","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},"volume":null,"type":"article","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5069762549","display_name":"Paulo Amaral","orcid":"https://orcid.org/0000-0002-6696-5142","observed_orcids":["https://orcid.org/0000-0002-6696-5142"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Paulo Amaral","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-6696-5142","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5069762549"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.01162539,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9487000107765198,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9487000107765198,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.03099999949336052,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.004800000227987766,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/non-coding-rna","display_name":"non-coding RNA","score":0.9739999771118164},{"id":"https://openalex.org/keywords/long-non-coding-rna","display_name":"long non-coding RNA","score":0.9559999704360962},{"id":"https://openalex.org/keywords/mouse-embryonic-stem-cells","display_name":"mouse embryonic stem cells","score":0.8100000023841858},{"id":"https://openalex.org/keywords/embryoid-body-differentiation","display_name":"embryoid body differentiation","score":0.8920000195503235},{"id":"https://openalex.org/keywords/mesoderm-differentiation","display_name":"mesoderm differentiation","score":0.8669999837875366},{"id":"https://openalex.org/keywords/h3k4me3","display_name":"H3K4me3","score":0.9139999747276306},{"id":"https://openalex.org/keywords/mll1","display_name":"MLL1","score":0.9750000238418579},{"id":"https://openalex.org/keywords/homeobox-genes","display_name":"homeobox genes","score":0.6539999842643738},{"id":"https://openalex.org/keywords/evx1","display_name":"Evx1","score":0.7459999918937683},{"id":"https://openalex.org/keywords/dlx-genes","display_name":"Dlx genes","score":0.871999979019165},{"id":"https://openalex.org/keywords/sox2","display_name":"SOX2","score":0.718999981880188},{"id":"https://openalex.org/keywords/pluripotency","display_name":"pluripotency","score":0.6340000033378601},{"id":"https://openalex.org/keywords/chromatin-regulation","display_name":"chromatin regulation","score":0.5580000281333923},{"id":"https://openalex.org/keywords/rna-expression-profiling","display_name":"RNA expression profiling","score":0.41999998688697815},{"id":"https://openalex.org/keywords/histone-methyltransferase","display_name":"histone methyltransferase","score":0.4259999990463257}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8174358606338501},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.6852750182151794},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5614069104194641},{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.5368950963020325},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5165457129478455},{"id":"https://openalex.org/C62203573","wikidata":"https://www.wikidata.org/wiki/Q15087973","display_name":"Long non-coding RNA","level":4,"score":0.5061551928520203},{"id":"https://openalex.org/C145059251","wikidata":"https://www.wikidata.org/wiki/Q310899","display_name":"microRNA","level":3,"score":0.45384281873703003},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4401888847351074},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.4342155158519745},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.430203914642334},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.4157913625240326},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.41398999094963074},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3861429691314697}],"mesh":[],"locations_count":1,"locations":[{"id":"mag:207474797","doi":null,"is_oa":false,"landing_page_url":"https://espace.library.uq.edu.au/view/UQ:262118","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W29733428","https://openalex.org/W2156392314","https://openalex.org/W7100012435","https://openalex.org/W2046312743","https://openalex.org/W1999746344","https://openalex.org/W2920998633","https://openalex.org/W2947356530","https://openalex.org/W4226087750","https://openalex.org/W2198059726","https://openalex.org/W2170094897"],"abstract_inverted_index":{"Although":[0],"only":[1],"a":[2,18,147,172,289,363,388,423,461,503,531,540,568],"small":[3],"fraction":[4],"of":[5,21,35,37,63,71,77,87,91,119,127,144,181,185,212,263,327,362,390,426,437,444,499,505,555,567,572,579,589,599,639,670,692,722,737],"the":[6,69,75,81,88,92,117,124,138,141,179,213,272,328,344,372,429,438,553,565,587,590,594,616,636,652,667,671,693,723,731,734],"mammalian":[7,420,672],"genome":[8],"comprises":[9],"annotated":[10],"protein-coding":[11,221],"sequences,":[12],"transcriptomic":[13],"studies":[14],"have":[15,56,224,407,648],"demonstrated":[16],"that":[17,40,102,223,244,298,356,524,537,607,659,745],"large":[19],"proportion":[20],"its":[22],"length":[23],"is":[24,100,278,342,360,539,581,603,702],"transcribed":[25,246],"in":[26,68,227,271,280,322,331,339,351,387,416,428,434,454,457,530,559,615,628,645,655,682,704,714,717,741],"different":[27,38,506,680,742],"cell":[28,162,229,400,684],"types.":[29],"Such":[30],"pervasive":[31],"transcription":[32,207],"generates":[33],"hundreds":[34],"thousands":[36],"RNAs":[39,105,128,193,215,469,490,507,545,556,575,613,710,739],"lack":[41],"substantial":[42],"open":[43],"reading":[44],"frames,":[45],"and":[46,84,98,115,121,205,256,275,300,313,378,397,411,419,477,551,584,597,632,642,677,686,699],"are":[47,95,245,268,303,320,674,746],"broadly":[48],"defined":[49],"as":[50,137,164,253,512,514,707,709],"\u201cnoncoding":[51],"RNAs\u201d":[52],"(ncRNAs).":[53],"Biological":[54],"roles":[55,226,453,681,713],"been":[57,649],"assigned":[58],"to":[59,107,113,122,153,249,383,406,412,448,467,543,582,585,665],"an":[60,604],"increasing":[61],"number":[62,389,504],"individually":[64],"characterized":[65,195,695],"ncRNAs,":[66,184,661],"notably":[67],"regulation":[70,456,716],"gene":[72,260,324,374],"expression":[73,82,118,158,176,380,427,700],"at":[74,309],"level":[76],"chromatin":[78,130,200,317,455,480,549,749],"structure.":[79,750],"However,":[80],"patterns":[83,701],"functional":[85,284,640],"properties":[86],"vast":[89],"majority":[90],"novel":[93,241,290],"transcripts":[94,450,501],"still":[96],"unexplored,":[97],"it":[99],"likely":[101,678],"many":[103,660],"more":[104,352],"remain":[106],"be":[108,384,413],"discovered.":[109],"This":[110],"thesis":[111,657],"aimed":[112,447],"identify":[114,449],"characterize":[116],"ncRNAs":[120,243,302,329,647,696],"investigate":[123],"global":[125],"association":[126],"with":[129,220,305,366,371,422,451,474,478,510,526,547,711],"using":[131,288],"mouse":[132,160,273,332,395],"embryonic":[133],"stem":[134,399],"(ES)":[135],"cells":[136],"model.":[139],"In":[140,286,460],"first":[142,694],"part":[143,361,443],"this":[145,276,357,445,656],"work,":[146],"custom":[148],"microarray":[149],"platform":[150],"was":[151,296,349,403],"used":[152,465],"survey":[154],"long":[155,573,611],"ncRNA":[156],"(lncRNA)":[157],"during":[159,394],"ES":[161,228,333,396,458,683,718],"differentiation":[163],"embryoid":[165],"bodies":[166],"(EBs)":[167],"into":[168],"mesoderm":[169],"lineages":[170],"over":[171,621],"16-day":[173],"time-course.":[174],"The":[175,441,577,601,720],"profiling":[177],"allowed":[178,552],"identification":[180,554,736],"945":[182],"expressed":[183,214,330],"which":[186,319,482,618,646,662],"174":[187],"were":[188,194,216,235,381,491],"significantly":[189],"differentially":[190,385],"expressed.":[191],"Expressed":[192],"by":[196,494,748],"combining":[197],"available":[198],"genome-wide":[199,532],"state":[201],"maps,":[202],"genomic":[203],"context":[204],"promoter":[206],"factor":[208],"binding":[209],"sites.":[210],"Many":[211],"found":[217,297,382,405],"genomically":[218],"associated":[219,304,370,473,509,546],"loci":[222],"important":[225],"pluripotency":[230,345],"or":[231,471],"differentiation.":[232,401],"Selected":[233],"lncRNAs":[234,627],"chosen":[236],"for":[237,570,610,733],"further":[238],"characterization,":[239],"including":[240,393,433],"spliced":[242,358],"antisense":[247],"(\u2018as\u2019)":[248],"homeobox":[250],"genes,":[251],"such":[252],"Evx1,":[254],"Hoxb5/6":[255],"all":[257],"three":[258],"Dlx":[259],"clusters.":[261],"Some":[262],"these":[264,500],"sense-antisense":[265],"RNA":[266,359,485,519],"pairs":[267],"spatially":[269],"co-expressed":[270],"embryo":[274],"co-regulation":[277],"maintained":[279],"adult":[281],"tissues,":[282],"indicating":[283],"relationships.":[285],"addition,":[287],"RNA-chromatin":[291],"immunoprecipitation":[292],"(RNA-ChIP)":[293],"technique,":[294],"evidence":[295],"Evx1as":[299],"Hoxb5/6Aas":[301],"histone":[306,314,475],"H3":[307,476],"trimethylated":[308],"lysine":[310],"4":[311],"(H3K4me3)":[312],"methyltransferase":[315],"MLL1":[316],"fractions,":[318],"involved":[321,558,740],"homeotic":[323],"activation.":[325],"One":[326],"cells,":[334],"Sox2":[335,347,373,377],"overlapping":[336],"transcript":[337],"(Sox2ot),":[338,706],"whose":[340,697],"intron":[341],"embedded":[343],"regulator":[346],"gene,":[348],"analyzed":[350,391],"detail.":[353],"We":[354],"observed":[355],"complex":[364],"locus":[365],"several":[367,435],"regulated":[368,386,415,676],"isoforms":[369],"throughout":[375],"vertebrates.":[376],"Sox2ot":[379,402],"systems,":[392],"neural":[398],"also":[404,729],"highly":[408],"conserved":[409,703],"promoters":[410],"dynamically":[414],"fish,":[417],"chicken":[418],"development,":[421],"consistent":[424],"pattern":[425],"central":[430],"nervous":[431],"system,":[432],"regions":[436],"human":[439],"brain.":[440],"second":[442],"work":[446],"potential":[452,712],"cells.":[459,719],"pilot":[462],"study,":[463],"I":[464,563],"RNA-ChIP":[466,538],"co-purify":[468],"directly":[470],"indirectly":[472],"H3K4me3":[479,528],"domains,":[481],"specifically":[483,675],"mark":[484],"Polymerase":[486],"II":[487],"promoters.":[488],"These":[489,534,689],"subsequently":[492],"identified":[493],"deep":[495],"sequencing":[496],"(\u201cRNA-ChIP-seq\u201d).":[497],"Analysis":[498],"revealed":[502],"potentially":[508,557],"chromatin,":[511],"well":[513,708],"~6":[515],"thousand":[516],"discrete":[517],"short":[518],"clusters":[520],"(averaging":[521],"<200":[522],"nt)":[523],"co-localized":[525],"mapped":[527],"domains":[529,550],"manner.":[533],"results":[535,653],"indicate":[536],"useful":[541],"method":[542],"isolate":[544],"specific":[548],"transcriptional":[560],"regulation.":[561],"Finally,":[562],"describe":[564],"preparation":[566],"database":[569,602],"annotation":[571],"noncoding":[574],"(\u201clncRNAdb\u201d).":[576],"goal":[578],"lncRNAdb":[580],"organize":[583],"increase":[586],"accessibility":[588],"data":[591],"resulting":[592],"from":[593],"rapid":[595],"discovery":[596],"characterization":[598],"lncRNAs.":[600],"online":[605],"resource":[606],"compiles":[608],"information":[609],"regulatory":[612,738],"described":[614],"literature,":[617],"currently":[619],"contains":[620],"one":[622,691],"hundred":[623],"fifty":[624],"manually":[625],"curated":[626],"unicellular":[629],"eukaryotes,":[630],"plants,":[631],"animals.":[633],"LncRNAdb":[634],"highlights":[635],"extensive":[637],"array":[638],"mechanisms":[641],"biological":[643],"processes":[644,744],"involved.":[650],"Collectively,":[651],"obtained":[654],"show":[658],"increasingly":[663],"appear":[664],"represent":[666],"primary":[668],"output":[669],"genome,":[673],"play":[679],"biology":[685],"developmental":[687],"processes.":[688],"include":[690],"structure":[698],"vertebrates":[705],"epigenetic":[715],"establishment":[721],"RNA-ChIP-seq":[724],"methodology":[725],"introduced":[726],"here":[727],"may":[728],"pave":[730],"way":[732],"targeted":[735],"molecular":[743],"influenced":[747]},"counts_by_year":[],"updated_date":"2026-09-12T09:15:50.089291","created_date":"2016-06-24T00:00:00"}
