{"id":"https://openalex.org/W2116244141","doi":null,"title":"Comparative Developmental Transcriptomics of Echinoderms","display_name":"Comparative Developmental Transcriptomics of Echinoderms","publication_year":2012,"publication_date":"2012-01-01","ids":{"openalex":"https://openalex.org/W2116244141","mag":"2116244141"},"language":"en","primary_location":{"id":"pmh:oai:digitalcommons.usf.edu:etd-5441","doi":null,"is_oa":true,"landing_page_url":"https://digitalcommons.usf.edu/etd/4245","pdf_url":"https://digitalcommons.usf.edu/context/etd/article/5441/viewcontent/etd__4245.pdf","source":{"id":"https://openalex.org/S4377196272","display_name":"Digital Commons - University of South Florida (University of South Florida)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2613432","host_organization_name":"University of South Florida","host_organization_lineage":["https://openalex.org/I2613432"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"USF Tampa Graduate Theses and Dissertations","raw_type":"dissertation"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://digitalcommons.usf.edu/context/etd/article/5441/viewcontent/etd__4245.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085379627","display_name":"Roy Vaughn","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Roy Vaughn","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5085379627"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"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/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.9922000169754028,"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"}},"topics":[{"id":"https://openalex.org/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.9922000169754028,"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/T12841","display_name":"Echinoderm biology and ecology","score":0.006000000052154064,"subfield":{"id":"https://openalex.org/subfields/1104","display_name":"Aquatic Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12142","display_name":"Marine Invertebrate Physiology and Ecology","score":0.0005000000237487257,"subfield":{"id":"https://openalex.org/subfields/1103","display_name":"Animal Science and Zoology"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/ophiuroidea","display_name":"Ophiuroidea","score":0.746999979019165},{"id":"https://openalex.org/keywords/sea-urchins","display_name":"sea urchins","score":0.9210000038146973},{"id":"https://openalex.org/keywords/strongylocentrotus-purpuratus","display_name":"Strongylocentrotus purpuratus","score":0.9890000224113464},{"id":"https://openalex.org/keywords/gastrula","display_name":"gastrula","score":0.8550000190734863},{"id":"https://openalex.org/keywords/germ-layer-specification","display_name":"germ layer specification","score":0.843999981880188},{"id":"https://openalex.org/keywords/gene-regulatory-networks","display_name":"gene regulatory networks","score":0.9929999709129333},{"id":"https://openalex.org/keywords/convergent-evolution","display_name":"convergent evolution","score":0.718999981880188},{"id":"https://openalex.org/keywords/transcription-factors","display_name":"transcription factors","score":0.5920000076293945},{"id":"https://openalex.org/keywords/transcriptome","display_name":"transcriptome","score":0.36399999260902405}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4711053967475891},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.43673160672187805},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.37491047382354736},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.346259742975235},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.3342704176902771},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14204803109169006},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11559224128723145},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:digitalcommons.usf.edu:etd-5441","doi":null,"is_oa":true,"landing_page_url":"https://digitalcommons.usf.edu/etd/4245","pdf_url":"https://digitalcommons.usf.edu/context/etd/article/5441/viewcontent/etd__4245.pdf","source":{"id":"https://openalex.org/S4377196272","display_name":"Digital Commons - University of South Florida (University of South Florida)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2613432","host_organization_name":"University of South Florida","host_organization_lineage":["https://openalex.org/I2613432"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"USF Tampa Graduate Theses and Dissertations","raw_type":"dissertation"},{"id":"pmh:oai:scholarcommons.usf.edu:etd-5441","doi":null,"is_oa":true,"landing_page_url":"https://scholarcommons.usf.edu/etd/4245","pdf_url":"https://scholarcommons.usf.edu/cgi/viewcontent.cgi?article=5441&context=etd","source":{"id":"https://openalex.org/S4377196272","display_name":"Digital Commons - University of South Florida (University of South Florida)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2613432","host_organization_name":"University of South Florida","host_organization_lineage":["https://openalex.org/I2613432"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Graduate Theses and Dissertations","raw_type":"text"},{"id":"mag:2116244141","doi":null,"is_oa":false,"landing_page_url":"https://digitalcommons.usf.edu/cgi/viewcontent.cgi?article=5441&context=etd","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":{"id":"pmh:oai:digitalcommons.usf.edu:etd-5441","doi":null,"is_oa":true,"landing_page_url":"https://digitalcommons.usf.edu/etd/4245","pdf_url":"https://digitalcommons.usf.edu/context/etd/article/5441/viewcontent/etd__4245.pdf","source":{"id":"https://openalex.org/S4377196272","display_name":"Digital Commons - University of South Florida (University of South Florida)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2613432","host_organization_name":"University of South Florida","host_organization_lineage":["https://openalex.org/I2613432"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"USF Tampa Graduate Theses and Dissertations","raw_type":"dissertation"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G5112598495","display_name":"Evolution of the Genes Involved In Formation of the Echinoderm Embryonic Skeleton","funder_award_id":"0909797","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2116244141.pdf","grobid_xml":"https://content.openalex.org/works/W2116244141.grobid-xml"},"referenced_works_count":149,"referenced_works":["https://openalex.org/W1497123013","https://openalex.org/W1507944481","https://openalex.org/W1533061131","https://openalex.org/W1606273823","https://openalex.org/W1701092691","https://openalex.org/W1783666737","https://openalex.org/W1874829192","https://openalex.org/W1892575185","https://openalex.org/W1966021458","https://openalex.org/W1966469846","https://openalex.org/W1968068346","https://openalex.org/W1970035070","https://openalex.org/W1973139865","https://openalex.org/W1973223713","https://openalex.org/W1973256028","https://openalex.org/W1974014232","https://openalex.org/W1975542294","https://openalex.org/W1976841360","https://openalex.org/W1978048734","https://openalex.org/W1978732075","https://openalex.org/W1979068398","https://openalex.org/W1980477105","https://openalex.org/W1980882917","https://openalex.org/W1981348283","https://openalex.org/W1983089543","https://openalex.org/W1984984154","https://openalex.org/W1985009227","https://openalex.org/W1987532345","https://openalex.org/W1987746335","https://openalex.org/W1988102605","https://openalex.org/W1989938007","https://openalex.org/W1990453950","https://openalex.org/W1990742741","https://openalex.org/W1991195375","https://openalex.org/W1991941177","https://openalex.org/W1994326863","https://openalex.org/W1995207946","https://openalex.org/W1996892469","https://openalex.org/W1997794139","https://openalex.org/W1998342476","https://openalex.org/W2002055282","https://openalex.org/W2002928212","https://openalex.org/W2004507679","https://openalex.org/W2005694235","https://openalex.org/W2006205550","https://openalex.org/W2008664813","https://openalex.org/W2009877718","https://openalex.org/W2009883127","https://openalex.org/W2012639536","https://openalex.org/W2015858554","https://openalex.org/W2016530350","https://openalex.org/W2016907728","https://openalex.org/W2017132951","https://openalex.org/W2018455039","https://openalex.org/W2019433333","https://openalex.org/W2023168496","https://openalex.org/W2023256299","https://openalex.org/W2024685686","https://openalex.org/W2024713711","https://openalex.org/W2025121053","https://openalex.org/W2028377604","https://openalex.org/W2031766495","https://openalex.org/W2034298458","https://openalex.org/W2035209944","https://openalex.org/W2035949664","https://openalex.org/W2037112883","https://openalex.org/W2039778763","https://openalex.org/W2040952171","https://openalex.org/W2041766916","https://openalex.org/W2042155385","https://openalex.org/W2044001472","https://openalex.org/W2044247659","https://openalex.org/W2049485508","https://openalex.org/W2051642959","https://openalex.org/W2052246603","https://openalex.org/W2053831990","https://openalex.org/W2054646046","https://openalex.org/W2056618354","https://openalex.org/W2057195804","https://openalex.org/W2059364511","https://openalex.org/W2059529537","https://openalex.org/W2060399360","https://openalex.org/W2061838418","https://openalex.org/W2067680168","https://openalex.org/W2068207277","https://openalex.org/W2069674573","https://openalex.org/W2071148354","https://openalex.org/W2078214291","https://openalex.org/W2080059178","https://openalex.org/W2085754302","https://openalex.org/W2086889826","https://openalex.org/W2087887426","https://openalex.org/W2091685617","https://openalex.org/W2092659352","https://openalex.org/W2094116868","https://openalex.org/W2095847047","https://openalex.org/W2100228967","https://openalex.org/W2100883860","https://openalex.org/W2101043145","https://openalex.org/W2102631576","https://openalex.org/W2102660198","https://openalex.org/W2103017472","https://openalex.org/W2110438893","https://openalex.org/W2111128689","https://openalex.org/W2111237039","https://openalex.org/W2112138896","https://openalex.org/W2112583319","https://openalex.org/W2114541039","https://openalex.org/W2116384301","https://openalex.org/W2116921512","https://openalex.org/W2120352535","https://openalex.org/W2121738029","https://openalex.org/W2122538595","https://openalex.org/W2123445833","https://openalex.org/W2123647329","https://openalex.org/W2123747127","https://openalex.org/W2124805860","https://openalex.org/W2125012054","https://openalex.org/W2126505440","https://openalex.org/W2127938895","https://openalex.org/W2129588731","https://openalex.org/W2129780380","https://openalex.org/W2129829180","https://openalex.org/W2134363076","https://openalex.org/W2135929304","https://openalex.org/W2137646798","https://openalex.org/W2137652608","https://openalex.org/W2140755714","https://openalex.org/W2142237694","https://openalex.org/W2146111983","https://openalex.org/W2147850720","https://openalex.org/W2149028985","https://openalex.org/W2151364836","https://openalex.org/W2152973976","https://openalex.org/W2153335610","https://openalex.org/W2153590739","https://openalex.org/W2155606054","https://openalex.org/W2156092712","https://openalex.org/W2157523980","https://openalex.org/W2158422725","https://openalex.org/W2158714788","https://openalex.org/W2159167011","https://openalex.org/W2159482845","https://openalex.org/W2165937624","https://openalex.org/W2167934696","https://openalex.org/W2184122648","https://openalex.org/W2210587626","https://openalex.org/W2213529608","https://openalex.org/W6981957009"],"related_works":["https://openalex.org/W2152908094","https://openalex.org/W2736562665","https://openalex.org/W1521511568","https://openalex.org/W2598020765","https://openalex.org/W2746211122","https://openalex.org/W2994561226","https://openalex.org/W2296889231","https://openalex.org/W2338854182","https://openalex.org/W3198456384","https://openalex.org/W2234352900"],"abstract_inverted_index":{"The":[0,216],"gastrula":[1,139,170,258],"stage":[2,233],"represents":[3,347],"the":[4,10,19,25,31,35,39,62,78,110,126,130,138,165,175,182,199,212,228,257,277,284,311,334,379,385,388,398,412,422,448,452,473,491,504],"point":[5,18],"in":[6,52,57,117,157,181,190,211,234,245,294,341,358,392,397,417,430,451,467,482],"development":[7,108,369],"at":[8,256,280,463],"which":[9,196,383],"three":[11],"primary":[12],"germ":[13,26,295],"layers":[14,27],"diverge.":[15],"At":[16],"this":[17,408],"gene":[20,202,380],"regulatory":[21,203,307,381],"networks":[22,47,204,382],"that":[23,33,83,93,152,219,242,318,329,337,460],"specify":[24],"are":[28,92,96,105,209,239,292,363,461],"established":[29],"and":[30,101,132,146,184,262,273,344,370,376,436,456,470,479,519],"genes":[32,156,162,179,251,278,287,317],"define":[34],"differentiated":[36],"states":[37],"of":[38,61,70,80,119,141,178,198,206,268,271,276,283,303,305,330,353,364,373,387,400,407,421,433,447,458,475,487,506],"tissues":[40],"have":[41,48,173,265],"begun":[42],"to":[43,86,109,154,187,227,310,367,427],"be":[44],"activated.":[45],"These":[46],"been":[49],"well":[50],"characterized":[51,174],"sea":[53,74,166,191,263,289,331,342,434,453,468],"urchins,":[54],"but":[55],"not":[56,480],"other":[58,488],"echinoderms.":[59],"Embryos":[60],"brittle":[63,149,248,285,345,423,483],"star":[64,150,249,286,424,440,484],"Ophiocoma":[65,142,425],"wendtii":[66,143,214,426],"share":[67,274],"a":[68,222,231,299,354,437],"number":[69],"developmental":[71,120,246,465,509],"features":[72],"with":[73,164,490,495,512],"urchin":[75,167,290,454],"embryos,":[76],"including":[77,160],"ingression":[79],"mesenchyme":[81],"cells":[82,104],"give":[84],"rise":[85],"an":[87],"embryonic":[88,235,338,389],"skeleton.":[89],"Notable":[90],"differences":[91,133,241,492],"no":[94,102],"micromeres":[95],"formed":[97,106],"during":[98,107],"cleavage":[99],"divisions":[100],"pigment":[103],"pluteus":[111],"larva":[112],"stage.":[113,259],"More":[114],"subtle":[115],"changes":[116,244],"timing":[118],"events":[121],"also":[122,240,315],"occur.":[123],"To":[124,403],"explore":[125],"molecular":[127],"basis":[128],"for":[129,444,503],"similarities":[131],"between":[134],"these":[135,393],"two":[136,431],"echinoderms,":[137,489,517],"transcriptome":[140,183],"was":[144],"sequenced":[145],"characterized.\\nI":[147],"identified":[148],"transcripts":[151],"correspond":[153],"3385":[155],"existing":[158],"databases,":[159],"1863":[161],"shared":[163,223,355,515],"Strongylocentrotus":[168],"purpuratus":[169,208],"transcriptome.":[171,313],"I":[172,193,314,410],"functional":[176,254],"classes":[177,255],"present":[180,416],"compared":[185,309,411],"them":[186],"those":[188,428,459,486],"found":[189,429,443,478,481],"urchin.":[192],"then":[194],"examined":[195],"members":[197],"germ-layer":[200],"specific":[201],"(GRNs)":[205],"S.":[207],"expressed":[210,279,462],"O.":[213],"gastrula.":[215,281],"results":[217],"indicate":[218],"there":[220,238],"is":[221],"\"genetic":[224],"toolkit\"":[225],"central":[226,365],"echinoderm":[229],"gastrula,":[230],"key":[232,306],"development,":[236],"though":[237],"reflect":[243],"processes.\\nThe":[247],"expresses":[250],"representing":[252],"all":[253],"Brittle":[260,439],"stars":[261,346],"urchins":[264,343,435,469],"comparable":[266],"numbers":[267],"each":[269],"class":[270],"genes,":[272],"many":[275],"Examination":[282],"whose":[288,323],"orthologs":[291],"utilized":[293,357],"layer":[296],"specification":[297],"reveals":[298],"relatively":[300],"higher":[301],"level":[302],"conservation":[304],"components":[308],"overall":[312],"identify":[316],"were":[319,442],"either":[320],"lost":[321],"or":[322],"temporal":[324],"expression":[325,375],"has":[326],"diverged":[327],"from":[328],"urchins.":[332],"Overall,":[333,472],"data":[335],"suggest":[336],"skeleton":[339,360],"formation":[340],"convergent":[348],"evolution":[349],"by":[350],"independent":[351],"cooptation":[352],"pathway":[356],"adult":[359],"formation.\\nTranscription":[361],"factors":[362,450,477],"importance":[366],"both":[368],"evolution.":[371],"Patterns":[372],"their":[374],"interactions":[377],"form":[378],"control":[384],"building":[386],"body.":[390],"Alterations":[391],"patterns":[394,474],"can":[395],"result":[396],"construction":[399],"altered":[401],"bodies.":[402],"help":[404],"increase":[405],"understanding":[406],"process,":[409],"transcription":[413,449,476],"factor":[414],"mRNAs":[415],"early":[418],"gastrula-stage":[419],"embryos":[420],"species":[432],"starfish.":[438,471],"homologs":[441],"one":[445],"third":[446],"genome":[455],"half":[457],"equivalent":[464],"stages":[466],"resemble":[485],"largely":[493],"consistent":[494],"morphological":[496],"differences.":[497],"This":[498],"study":[499],"provides":[500],"further":[501],"evidence":[502],"existence":[505],"deeply":[507],"conserved":[508],"genetic":[510],"processes,":[511],"various":[513],"elements":[514],"among":[516],"deuterostomes,":[518],"metazoans.":[520]},"counts_by_year":[],"updated_date":"2026-10-01T08:54:57.152042","created_date":"2016-06-24T00:00:00"}