Ontology type: schema:ScholarlyArticle Open Access: True
2010-05
AUTHORSCole Trapnell, Brian A Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold, Lior Pachter
ABSTRACTHigh-throughput mRNA sequencing (RNA-Seq) promises simultaneous transcript discovery and abundance estimation. However, this would require algorithms that are not restricted by prior gene annotations and that account for alternative transcription and splicing. Here we introduce such algorithms in an open-source software program called Cufflinks. To test Cufflinks, we sequenced and analyzed >430 million paired 75-bp RNA-Seq reads from a mouse myoblast cell line over a differentiation time series. We detected 13,692 known transcripts and 3,724 previously unannotated ones, 62% of which are supported by independent expression data or by homologous genes in other species. Over the time series, 330 genes showed complete switches in the dominant transcription start site (TSS) or splice isoform, and we observed more subtle shifts in 1,304 other genes. These results suggest that Cufflinks can illuminate the substantial regulatory flexibility and complexity in even this well-studied model of muscle development and that it can improve transcriptome-based genome annotation. More... »
PAGES511
http://scigraph.springernature.com/pub.10.1038/nbt.1621
DOIhttp://dx.doi.org/10.1038/nbt.1621
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1031035095
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/20436464
JSON-LD is the canonical representation for SciGraph data.
TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT
[
{
"@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json",
"about": [
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Genetics",
"type": "DefinedTerm"
},
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Biological Sciences",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Algorithms",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Animals",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Cell Differentiation",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Cell Line",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Gene Expression Profiling",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Genome",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Mice",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Oligonucleotide Array Sequence Analysis",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Protein Isoforms",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Proto-Oncogene Proteins c-myc",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "RNA, Messenger",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Sequence Analysis, RNA",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Software",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"alternateName": "University of California, Berkeley",
"id": "https://www.grid.ac/institutes/grid.47840.3f",
"name": [
"Department of Computer Science, University of Maryland, College Park, Maryland, USA.",
"Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA.",
"Department of Mathematics, University of California, Berkeley, California, USA."
],
"type": "Organization"
},
"familyName": "Trapnell",
"givenName": "Cole",
"id": "sg:person.01247375013.30",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01247375013.30"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "California Institute of Technology",
"id": "https://www.grid.ac/institutes/grid.20861.3d",
"name": [
"Division of Biology and Beckman Institute, California Institute of Technology, Pasadena, California, USA."
],
"type": "Organization"
},
"familyName": "Williams",
"givenName": "Brian A",
"id": "sg:person.0741140331.06",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0741140331.06"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of Maryland, College Park",
"id": "https://www.grid.ac/institutes/grid.164295.d",
"name": [
"Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA."
],
"type": "Organization"
},
"familyName": "Pertea",
"givenName": "Geo",
"id": "sg:person.01024612415.46",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01024612415.46"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "California Institute of Technology",
"id": "https://www.grid.ac/institutes/grid.20861.3d",
"name": [
"Division of Biology and Beckman Institute, California Institute of Technology, Pasadena, California, USA."
],
"type": "Organization"
},
"familyName": "Mortazavi",
"givenName": "Ali",
"id": "sg:person.0673025131.06",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0673025131.06"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "California Institute of Technology",
"id": "https://www.grid.ac/institutes/grid.20861.3d",
"name": [
"Division of Biology and Beckman Institute, California Institute of Technology, Pasadena, California, USA."
],
"type": "Organization"
},
"familyName": "Kwan",
"givenName": "Gordon",
"id": "sg:person.0774300251.64",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0774300251.64"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Washington University in St. Louis",
"id": "https://www.grid.ac/institutes/grid.4367.6",
"name": [
"Genome Sciences Center, Washington University in St. Louis, St. Louis, Missouri, USA."
],
"type": "Organization"
},
"familyName": "van Baren",
"givenName": "Marijke J",
"id": "sg:person.01042023041.45",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01042023041.45"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of Maryland, College Park",
"id": "https://www.grid.ac/institutes/grid.164295.d",
"name": [
"Department of Computer Science, University of Maryland, College Park, Maryland, USA.",
"Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA."
],
"type": "Organization"
},
"familyName": "Salzberg",
"givenName": "Steven L",
"id": "sg:person.01223441713.02",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01223441713.02"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "California Institute of Technology",
"id": "https://www.grid.ac/institutes/grid.20861.3d",
"name": [
"Division of Biology and Beckman Institute, California Institute of Technology, Pasadena, California, USA."
],
"type": "Organization"
},
"familyName": "Wold",
"givenName": "Barbara J",
"id": "sg:person.01026162263.73",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01026162263.73"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of California, Berkeley",
"id": "https://www.grid.ac/institutes/grid.47840.3f",
"name": [
"Department of Mathematics, University of California, Berkeley, California, USA.",
"Department of Molecular and Cell Biology, University of California, Berkeley, California, USA.",
"Department of Computer Science, University of California, Berkeley, California, USA."
],
"type": "Organization"
},
"familyName": "Pachter",
"givenName": "Lior",
"id": "sg:person.0672165566.75",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0672165566.75"
],
"type": "Person"
}
],
"citation": [
{
"id": "sg:pub.10.1038/nature08195",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1007963177",
"https://doi.org/10.1038/nature08195"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature08195",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1007963177",
"https://doi.org/10.1038/nature08195"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature07638",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1009442631",
"https://doi.org/10.1038/nature07638"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pcbi.1000074",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1010292273"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nmeth.1371",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1011651858",
"https://doi.org/10.1038/nmeth.1371"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/bioinformatics/btp120",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1012425816"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/gb-2008-9-12-r175",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1016469219",
"https://doi.org/10.1186/gb-2008-9-12-r175"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1126/science.1141319",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1018702276"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/bioinformatics/btp352",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1023014918"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1128/mcb.6.5.1412",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1025601272"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1242/jcs.004739",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1025879815"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/bioinformatics/btp544",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1026453845"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature07509",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1029002744",
"https://doi.org/10.1038/nature07509"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature05676",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1030633547",
"https://doi.org/10.1038/nature05676"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1242/dev.01874",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1032416057"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/s0955-0674(96)80091-3",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1038486419"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/bioinformatics/btp113",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1044688303"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/bioinformatics/btp692",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1045138418"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nmeth.1226",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1045381177",
"https://doi.org/10.1038/nmeth.1226"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1101/gr.079558.108",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1045837493"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nmeth.1223",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1048586936",
"https://doi.org/10.1038/nmeth.1223"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/gb-2009-10-3-r25",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1049583368",
"https://doi.org/10.1186/gb-2009-10-3-r25"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/nar/gkg770",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1050668915"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature07672",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1051133532",
"https://doi.org/10.1038/nature07672"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1111/j.1432-0436.1977.tb01507.x",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1051515183"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/1471-2105-11-94",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1053091615",
"https://doi.org/10.1186/1471-2105-11-94"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1126/science.1158441",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1062457766"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.2307/1969503",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1069674881"
],
"type": "CreativeWork"
}
],
"datePublished": "2010-05",
"datePublishedReg": "2010-05-01",
"description": "High-throughput mRNA sequencing (RNA-Seq) promises simultaneous transcript discovery and abundance estimation. However, this would require algorithms that are not restricted by prior gene annotations and that account for alternative transcription and splicing. Here we introduce such algorithms in an open-source software program called Cufflinks. To test Cufflinks, we sequenced and analyzed >430 million paired 75-bp RNA-Seq reads from a mouse myoblast cell line over a differentiation time series. We detected 13,692 known transcripts and 3,724 previously unannotated ones, 62% of which are supported by independent expression data or by homologous genes in other species. Over the time series, 330 genes showed complete switches in the dominant transcription start site (TSS) or splice isoform, and we observed more subtle shifts in 1,304 other genes. These results suggest that Cufflinks can illuminate the substantial regulatory flexibility and complexity in even this well-studied model of muscle development and that it can improve transcriptome-based genome annotation.",
"genre": "research_article",
"id": "sg:pub.10.1038/nbt.1621",
"inLanguage": [
"en"
],
"isAccessibleForFree": true,
"isFundedItemOf": [
{
"id": "sg:grant.2529425",
"type": "MonetaryGrant"
},
{
"id": "sg:grant.2545461",
"type": "MonetaryGrant"
},
{
"id": "sg:grant.2519905",
"type": "MonetaryGrant"
},
{
"id": "sg:grant.2699343",
"type": "MonetaryGrant"
}
],
"isPartOf": [
{
"id": "sg:journal.1115214",
"issn": [
"1087-0156",
"1546-1696"
],
"name": "Nature Biotechnology",
"type": "Periodical"
},
{
"issueNumber": "5",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "28"
}
],
"name": "Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation",
"pagination": "511",
"productId": [
{
"name": "readcube_id",
"type": "PropertyValue",
"value": [
"93d984f48bd8806cf117d2f18bb9a253fdb7a71a5557f3278a3ff33017297c98"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"20436464"
]
},
{
"name": "nlm_unique_id",
"type": "PropertyValue",
"value": [
"9604648"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1038/nbt.1621"
]
},
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1031035095"
]
}
],
"sameAs": [
"https://doi.org/10.1038/nbt.1621",
"https://app.dimensions.ai/details/publication/pub.1031035095"
],
"sdDataset": "articles",
"sdDatePublished": "2019-04-10T13:00",
"sdLicense": "https://scigraph.springernature.com/explorer/license/",
"sdPublisher": {
"name": "Springer Nature - SN SciGraph project",
"type": "Organization"
},
"sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8659_00000435.jsonl",
"type": "ScholarlyArticle",
"url": "https://www.nature.com/articles/nbt.1621"
}
]Download the RDF metadata as: json-ld nt turtle xml License info
JSON-LD is a popular format for linked data which is fully compatible with JSON.
curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/nbt.1621'
N-Triples is a line-based linked data format ideal for batch operations.
curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/nbt.1621'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nbt.1621'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nbt.1621'
This table displays all metadata directly associated to this object as RDF triples.
291 TRIPLES
21 PREDICATES
69 URIs
34 LITERALS
22 BLANK NODES