Ontology type: schema:ScholarlyArticle Open Access: True
2008-09-17
AUTHORSYong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li, X Shirley Liu
ABSTRACTWe present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the shift size of ChIP-Seq tags, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, and is freely available. More... »
PAGESr137
http://scigraph.springernature.com/pub.10.1186/gb-2008-9-9-r137
DOIhttp://dx.doi.org/10.1186/gb-2008-9-9-r137
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1027608848
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/18798982
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/2008/06",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Biological Sciences",
"type": "DefinedTerm"
},
{
"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"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Algorithms",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Cell Line, Tumor",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Chromatin Immunoprecipitation",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Hepatocyte Nuclear Factor 3-alpha",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Humans",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Models, Genetic",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Oligonucleotide Array Sequence Analysis",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"alternateName": "Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, 44 Binney Street, 02115, Boston, MA, USA",
"id": "http://www.grid.ac/institutes/grid.38142.3c",
"name": [
"Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, 44 Binney Street, 02115, Boston, MA, USA"
],
"type": "Organization"
},
"familyName": "Zhang",
"givenName": "Yong",
"id": "sg:person.011774204647.95",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011774204647.95"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, 44 Binney Street, 02115, Boston, MA, USA",
"id": "http://www.grid.ac/institutes/grid.38142.3c",
"name": [
"Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, 44 Binney Street, 02115, Boston, MA, USA"
],
"type": "Organization"
},
"familyName": "Liu",
"givenName": "Tao",
"id": "sg:person.01032120140.34",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01032120140.34"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, 44 Binney Street, 02115, Boston, MA, USA",
"id": "http://www.grid.ac/institutes/grid.38142.3c",
"name": [
"Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, 44 Binney Street, 02115, Boston, MA, USA"
],
"type": "Organization"
},
"familyName": "Meyer",
"givenName": "Clifford A",
"id": "sg:person.010256757607.98",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010256757607.98"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 44 Binney Street, 02115, Boston, MA, USA",
"id": "http://www.grid.ac/institutes/None",
"name": [
"Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 44 Binney Street, 02115, Boston, MA, USA"
],
"type": "Organization"
},
"familyName": "Eeckhoute",
"givenName": "J\u00e9r\u00f4me",
"id": "sg:person.01316327660.80",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01316327660.80"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Gene Security Network, Inc., 2686 Middlefield Road, 94063, Redwood City, CA, USA",
"id": "http://www.grid.ac/institutes/grid.434549.b",
"name": [
"Gene Security Network, Inc., 2686 Middlefield Road, 94063, Redwood City, CA, USA"
],
"type": "Organization"
},
"familyName": "Johnson",
"givenName": "David S",
"id": "sg:person.01266373043.21",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01266373043.21"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Broad Institute of Harvard and MIT, 7 Cambridge Center, 02142, Cambridge, MA, USA",
"id": "http://www.grid.ac/institutes/grid.66859.34",
"name": [
"Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital and Department of Pathology, Harvard Medical School, 13th Street, 02129, Charlestown, MA, USA",
"Broad Institute of Harvard and MIT, 7 Cambridge Center, 02142, Cambridge, MA, USA"
],
"type": "Organization"
},
"familyName": "Bernstein",
"givenName": "Bradley E",
"id": "sg:person.0724604220.48",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0724604220.48"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Broad Institute of Harvard and MIT, 7 Cambridge Center, 02142, Cambridge, MA, USA",
"id": "http://www.grid.ac/institutes/grid.66859.34",
"name": [
"Broad Institute of Harvard and MIT, 7 Cambridge Center, 02142, Cambridge, MA, USA"
],
"type": "Organization"
},
"familyName": "Nusbaum",
"givenName": "Chad",
"id": "sg:person.01170225154.35",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01170225154.35"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Genetics, Stanford University Medical Center, 94305, Stanford, CA, USA",
"id": "http://www.grid.ac/institutes/grid.240952.8",
"name": [
"Department of Genetics, Stanford University Medical Center, 94305, Stanford, CA, USA"
],
"type": "Organization"
},
"familyName": "Myers",
"givenName": "Richard M",
"id": "sg:person.015633514702.89",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015633514702.89"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 44 Binney Street, 02115, Boston, MA, USA",
"id": "http://www.grid.ac/institutes/None",
"name": [
"Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 44 Binney Street, 02115, Boston, MA, USA"
],
"type": "Organization"
},
"familyName": "Brown",
"givenName": "Myles",
"id": "sg:person.015327711457.65",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015327711457.65"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Division of Biostatistics, Dan L Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, 77030, Houston, TX, USA",
"id": "http://www.grid.ac/institutes/grid.39382.33",
"name": [
"Division of Biostatistics, Dan L Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, 77030, Houston, TX, USA"
],
"type": "Organization"
},
"familyName": "Li",
"givenName": "Wei",
"id": "sg:person.014233762715.49",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014233762715.49"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, 44 Binney Street, 02115, Boston, MA, USA",
"id": "http://www.grid.ac/institutes/grid.38142.3c",
"name": [
"Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, 44 Binney Street, 02115, Boston, MA, USA"
],
"type": "Organization"
},
"familyName": "Liu",
"givenName": "X Shirley",
"id": "sg:person.01007325065.71",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01007325065.71"
],
"type": "Person"
}
],
"citation": [
{
"id": "sg:pub.10.1038/nature06008",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1036216819",
"https://doi.org/10.1038/nature06008"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature05329",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1052925490",
"https://doi.org/10.1038/nature05329"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ng1901",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1012239798",
"https://doi.org/10.1038/ng1901"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/gb-2007-8-8-r178",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1033745816",
"https://doi.org/10.1186/gb-2007-8-8-r178"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nmeth1068",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1036304799",
"https://doi.org/10.1038/nmeth1068"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/35054095",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1037596378",
"https://doi.org/10.1038/35054095"
],
"type": "CreativeWork"
}
],
"datePublished": "2008-09-17",
"datePublishedReg": "2008-09-17",
"description": "We present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the shift size of ChIP-Seq tags, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, and is freely available.",
"genre": "article",
"id": "sg:pub.10.1186/gb-2008-9-9-r137",
"inLanguage": "en",
"isAccessibleForFree": true,
"isFundedItemOf": [
{
"id": "sg:grant.7143531",
"type": "MonetaryGrant"
},
{
"id": "sg:grant.2529282",
"type": "MonetaryGrant"
},
{
"id": "sg:grant.2691239",
"type": "MonetaryGrant"
},
{
"id": "sg:grant.2667408",
"type": "MonetaryGrant"
},
{
"id": "sg:grant.2499023",
"type": "MonetaryGrant"
}
],
"isPartOf": [
{
"id": "sg:journal.1023439",
"issn": [
"1474-760X",
"1465-6906"
],
"name": "Genome Biology",
"publisher": "Springer Nature",
"type": "Periodical"
},
{
"issueNumber": "9",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "9"
}
],
"keywords": [
"model-based analysis",
"spatial resolution",
"analysis",
"analyzer",
"shift size",
"size",
"resolution",
"distribution",
"local biases",
"more robust predictions",
"robust predictions",
"prediction",
"peak-finding algorithm",
"algorithm",
"ChIP-seq data",
"data",
"MACS",
"short-read sequencers",
"sequencer",
"Genome Analyzer",
"tags",
"sites",
"Poisson distribution",
"biases",
"genome",
"ChIP-seq"
],
"name": "Model-based Analysis of ChIP-Seq (MACS)",
"pagination": "r137",
"productId": [
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1027608848"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1186/gb-2008-9-9-r137"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"18798982"
]
}
],
"sameAs": [
"https://doi.org/10.1186/gb-2008-9-9-r137",
"https://app.dimensions.ai/details/publication/pub.1027608848"
],
"sdDataset": "articles",
"sdDatePublished": "2022-05-20T07:24",
"sdLicense": "https://scigraph.springernature.com/explorer/license/",
"sdPublisher": {
"name": "Springer Nature - SN SciGraph project",
"type": "Organization"
},
"sdSource": "s3://com-springernature-scigraph/baseset/20220519/entities/gbq_results/article/article_460.jsonl",
"type": "ScholarlyArticle",
"url": "https://doi.org/10.1186/gb-2008-9-9-r137"
}
]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.10.1186/gb-2008-9-9-r137'
N-Triples is a line-based linked data format ideal for batch operations.
curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/gb-2008-9-9-r137'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/gb-2008-9-9-r137'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/gb-2008-9-9-r137'
This table displays all metadata directly associated to this object as RDF triples.
236 TRIPLES
22 PREDICATES
65 URIs
51 LITERALS
14 BLANK NODES