Tag-based approaches for transcriptome research and genome annotation View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2005-07

AUTHORS

Matthias Harbers, Piero Carninci

ABSTRACT

With the increasing number of whole genome sequences available, genomic research has shifted toward the annotation of functional elements and transcribed regions. Thus, the related field of transcriptome research requires accurate methods for the profiling of genes that are not biased by known sequence information, and that also allow for the identification of promoter regions. Starting with serial analysis of gene expression (SAGE), methods making use of short sequencing tags have greatly contributed to transcriptome studies. Here we review recent developments in the use of short sequencing tags in expression profiling, gene discovery and genome annotation. These tags are obtained from the 5' end of mRNAs, both terminal ends of mRNAs, or genomic regions. The 5' end-specific tags, with their ability to identify transcripts along with their transcriptional start sites, will be of particular interest for gene network studies and may become one of the most important approaches in systems biology. More... »

PAGES

495-502

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nmeth768

DOI

http://dx.doi.org/10.1038/nmeth768

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1006027429

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/15973418


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

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": "Animals", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Expressed Sequence Tags", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gene Expression Profiling", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genomics", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Humans", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Promoter Regions, Genetic", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Proteome", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sequence Analysis, DNA", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Systems Biology", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Transcription Factors", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Transcription, Genetic", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "name": [
            "K.K. Dnaform, Tsukuba Branch, 3-1 Chuo 8-chome, Ami Machi, Inashiki Gun, Ibaraki, 300-0332, Japan."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Harbers", 
        "givenName": "Matthias", 
        "id": "sg:person.0662427634.38", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0662427634.38"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "RIKEN", 
          "id": "https://www.grid.ac/institutes/grid.7597.c", 
          "name": [
            "Genome Science Laboratory, RIKEN, Wako main campus, Hirosawa 2-1 Wako, Japan."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Carninci", 
        "givenName": "Piero", 
        "id": "sg:person.01023710753.40", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01023710753.40"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1126/science.1075090", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001953109"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.873003", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1002115475"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.292.5518.929", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004753512"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0308384100", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005134437"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/30.1.207", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005297170"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gki085", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009501697"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/mcb.1.2.179", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009728814"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.bbrc.2004.07.200", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012298431"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0403514101", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013107285"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0014-5793(04)00018-3", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015721066"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt0502-508", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016616140", 
          "https://doi.org/10.1038/nbt0502-508"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt0502-508", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016616140", 
          "https://doi.org/10.1038/nbt0502-508"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.145100", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017491574"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.10.7.1051", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017945935"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1006/geno.1996.0567", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019249665"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkg763", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019401433"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1146/annurev.genom.2.1.343", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019815147"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0407387101", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026102531"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt998", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026949774", 
          "https://doi.org/10.1038/nbt998"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt998", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026949774", 
          "https://doi.org/10.1038/nbt998"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1462-5822.2004.00478.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027457227"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.2136655100", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028529038"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/76469", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028559169", 
          "https://doi.org/10.1038/76469"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/76469", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028559169", 
          "https://doi.org/10.1038/76469"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0076-6879(99)03004-9", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028617756"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth726", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030149986", 
          "https://doi.org/10.1038/nmeth726"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth726", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030149986", 
          "https://doi.org/10.1038/nmeth726"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkh937", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030573947"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt964", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030931723", 
          "https://doi.org/10.1038/nbt964"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt964", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030931723", 
          "https://doi.org/10.1038/nbt964"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gad.1256904", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031360678"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.2536670100", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032730078"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gki020", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035717041"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.2769804", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037481214"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth733", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038506370", 
          "https://doi.org/10.1038/nmeth733"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth733", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038506370", 
          "https://doi.org/10.1038/nmeth733"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.tibtech.2003.11.002", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039600578"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1103388", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042123507"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.1119703", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043471471"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0378-1119(94)90802-8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044144266"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0378-1119(94)90802-8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044144266"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0378-1119(00)00557-6", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044851927"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.2596504", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044936424"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature01266", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045627219", 
          "https://doi.org/10.1038/nature01266"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature01266", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045627219", 
          "https://doi.org/10.1038/nature01266"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.1414204", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045727851"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/16.11.953", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045857704"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1146/annurev.biochem.72.121801.161720", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045905529"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35057149", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046153445", 
          "https://doi.org/10.1038/35057149"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35057149", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046153445", 
          "https://doi.org/10.1038/35057149"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1108625", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046921907"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/25.17.3389", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047265454"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.tig.2003.09.014", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049684815"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.tig.2003.09.014", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049684815"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.2094104", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050487471"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.202610899", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050518611"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/mcb.15.6.3363", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053537361"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.270.5235.484", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062551479"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.280.5366.1077", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062561068"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.290.5499.2144", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062572479"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.306.5696.630", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062586440"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1074672793", 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1152/physiolgenomics.2001.6.2.57", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1074851182"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.2144/01315st04", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1074960954"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/j.1460-2075.1986.tb04631.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1079514447"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2005-07", 
    "datePublishedReg": "2005-07-01", 
    "description": "With the increasing number of whole genome sequences available, genomic research has shifted toward the annotation of functional elements and transcribed regions. Thus, the related field of transcriptome research requires accurate methods for the profiling of genes that are not biased by known sequence information, and that also allow for the identification of promoter regions. Starting with serial analysis of gene expression (SAGE), methods making use of short sequencing tags have greatly contributed to transcriptome studies. Here we review recent developments in the use of short sequencing tags in expression profiling, gene discovery and genome annotation. These tags are obtained from the 5' end of mRNAs, both terminal ends of mRNAs, or genomic regions. The 5' end-specific tags, with their ability to identify transcripts along with their transcriptional start sites, will be of particular interest for gene network studies and may become one of the most important approaches in systems biology.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1038/nmeth768", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": false, 
    "isPartOf": [
      {
        "id": "sg:journal.1033763", 
        "issn": [
          "1548-7091", 
          "1548-7105"
        ], 
        "name": "Nature Methods", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "7", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "2"
      }
    ], 
    "name": "Tag-based approaches for transcriptome research and genome annotation", 
    "pagination": "495-502", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "1cb62284a2f4eee8b39a72821418cff94facba4a8f6c595e8fa928a717dd69ea"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "15973418"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "101215604"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/nmeth768"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1006027429"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/nmeth768", 
      "https://app.dimensions.ai/details/publication/pub.1006027429"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-11T12:24", 
    "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/v90/0000000362_0000000362/records_87100_00000000.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://www.nature.com/articles/nmeth768"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

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/nmeth768'

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/nmeth768'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nmeth768'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nmeth768'


 

This table displays all metadata directly associated to this object as RDF triples.

294 TRIPLES      21 PREDICATES      95 URIs      32 LITERALS      20 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/nmeth768 schema:about N06b2f72398034515904350886e123a3c
2 N0c3d60af0b0f49d880678448483a4e91
3 N1be64e5b540244d8b2c58e32a76930c4
4 N4f97015d6204436ea9dafd1e75891c6d
5 N672b264c19e7406eb16cdaca5341c60d
6 N7bb6ae93f224449485deccf91b56853b
7 N8742d528c5da41b5afc1053ba1bb8f2b
8 N9523da7fa64c4c7288b653f6bd3b36d1
9 Nc7dfcf446a7748eba0a6556f83988068
10 Nca2e4ce67cab4df599e3225df9e52df3
11 Nf0ff39544f9f435eb71aa53cfb9d1ede
12 anzsrc-for:06
13 anzsrc-for:0604
14 schema:author N794433480be44748be2098cfa562258d
15 schema:citation sg:pub.10.1038/35057149
16 sg:pub.10.1038/76469
17 sg:pub.10.1038/nature01266
18 sg:pub.10.1038/nbt0502-508
19 sg:pub.10.1038/nbt964
20 sg:pub.10.1038/nbt998
21 sg:pub.10.1038/nmeth726
22 sg:pub.10.1038/nmeth733
23 https://app.dimensions.ai/details/publication/pub.1074672793
24 https://doi.org/10.1002/j.1460-2075.1986.tb04631.x
25 https://doi.org/10.1006/geno.1996.0567
26 https://doi.org/10.1016/0378-1119(94)90802-8
27 https://doi.org/10.1016/j.bbrc.2004.07.200
28 https://doi.org/10.1016/j.tibtech.2003.11.002
29 https://doi.org/10.1016/j.tig.2003.09.014
30 https://doi.org/10.1016/s0014-5793(04)00018-3
31 https://doi.org/10.1016/s0076-6879(99)03004-9
32 https://doi.org/10.1016/s0378-1119(00)00557-6
33 https://doi.org/10.1073/pnas.0308384100
34 https://doi.org/10.1073/pnas.0403514101
35 https://doi.org/10.1073/pnas.0407387101
36 https://doi.org/10.1073/pnas.202610899
37 https://doi.org/10.1073/pnas.2136655100
38 https://doi.org/10.1073/pnas.2536670100
39 https://doi.org/10.1093/bioinformatics/16.11.953
40 https://doi.org/10.1093/nar/25.17.3389
41 https://doi.org/10.1093/nar/30.1.207
42 https://doi.org/10.1093/nar/gkg763
43 https://doi.org/10.1093/nar/gkh937
44 https://doi.org/10.1093/nar/gki020
45 https://doi.org/10.1093/nar/gki085
46 https://doi.org/10.1101/gad.1256904
47 https://doi.org/10.1101/gr.10.7.1051
48 https://doi.org/10.1101/gr.1119703
49 https://doi.org/10.1101/gr.1414204
50 https://doi.org/10.1101/gr.145100
51 https://doi.org/10.1101/gr.2094104
52 https://doi.org/10.1101/gr.2596504
53 https://doi.org/10.1101/gr.2769804
54 https://doi.org/10.1101/gr.873003
55 https://doi.org/10.1111/j.1462-5822.2004.00478.x
56 https://doi.org/10.1126/science.1075090
57 https://doi.org/10.1126/science.1103388
58 https://doi.org/10.1126/science.1108625
59 https://doi.org/10.1126/science.270.5235.484
60 https://doi.org/10.1126/science.280.5366.1077
61 https://doi.org/10.1126/science.290.5499.2144
62 https://doi.org/10.1126/science.292.5518.929
63 https://doi.org/10.1126/science.306.5696.630
64 https://doi.org/10.1128/mcb.1.2.179
65 https://doi.org/10.1128/mcb.15.6.3363
66 https://doi.org/10.1146/annurev.biochem.72.121801.161720
67 https://doi.org/10.1146/annurev.genom.2.1.343
68 https://doi.org/10.1152/physiolgenomics.2001.6.2.57
69 https://doi.org/10.2144/01315st04
70 schema:datePublished 2005-07
71 schema:datePublishedReg 2005-07-01
72 schema:description With the increasing number of whole genome sequences available, genomic research has shifted toward the annotation of functional elements and transcribed regions. Thus, the related field of transcriptome research requires accurate methods for the profiling of genes that are not biased by known sequence information, and that also allow for the identification of promoter regions. Starting with serial analysis of gene expression (SAGE), methods making use of short sequencing tags have greatly contributed to transcriptome studies. Here we review recent developments in the use of short sequencing tags in expression profiling, gene discovery and genome annotation. These tags are obtained from the 5' end of mRNAs, both terminal ends of mRNAs, or genomic regions. The 5' end-specific tags, with their ability to identify transcripts along with their transcriptional start sites, will be of particular interest for gene network studies and may become one of the most important approaches in systems biology.
73 schema:genre research_article
74 schema:inLanguage en
75 schema:isAccessibleForFree false
76 schema:isPartOf Nb4e93f7f64a1431dad0ae2baa906adda
77 Nfde8300b633b41d7b39e4ab991d29527
78 sg:journal.1033763
79 schema:name Tag-based approaches for transcriptome research and genome annotation
80 schema:pagination 495-502
81 schema:productId N2dd15588d75a453e8ceffe0d42fb235c
82 N6c59a9a27465422a8db94bebca3ddb15
83 Na7a3f25058a34e13b45f6a67b4a0ec71
84 Nda569ba7e256419eb5f157b7e212476e
85 Ndf9ab1bf00644eb3bed64505a4fcda2e
86 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006027429
87 https://doi.org/10.1038/nmeth768
88 schema:sdDatePublished 2019-04-11T12:24
89 schema:sdLicense https://scigraph.springernature.com/explorer/license/
90 schema:sdPublisher N6c8e2443c5d44120894a74a0553a34d5
91 schema:url http://www.nature.com/articles/nmeth768
92 sgo:license sg:explorer/license/
93 sgo:sdDataset articles
94 rdf:type schema:ScholarlyArticle
95 N06b2f72398034515904350886e123a3c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
96 schema:name Sequence Analysis, DNA
97 rdf:type schema:DefinedTerm
98 N0c3d60af0b0f49d880678448483a4e91 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
99 schema:name Gene Expression Profiling
100 rdf:type schema:DefinedTerm
101 N1be64e5b540244d8b2c58e32a76930c4 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
102 schema:name Expressed Sequence Tags
103 rdf:type schema:DefinedTerm
104 N2dd15588d75a453e8ceffe0d42fb235c schema:name pubmed_id
105 schema:value 15973418
106 rdf:type schema:PropertyValue
107 N4f97015d6204436ea9dafd1e75891c6d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
108 schema:name Animals
109 rdf:type schema:DefinedTerm
110 N672b264c19e7406eb16cdaca5341c60d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
111 schema:name Humans
112 rdf:type schema:DefinedTerm
113 N6c59a9a27465422a8db94bebca3ddb15 schema:name nlm_unique_id
114 schema:value 101215604
115 rdf:type schema:PropertyValue
116 N6c8e2443c5d44120894a74a0553a34d5 schema:name Springer Nature - SN SciGraph project
117 rdf:type schema:Organization
118 N794433480be44748be2098cfa562258d rdf:first sg:person.0662427634.38
119 rdf:rest Nbb9cf352e2e8424d8689c8ece04e567c
120 N7b227a0c469649508637cf3b1aa4e469 schema:name K.K. Dnaform, Tsukuba Branch, 3-1 Chuo 8-chome, Ami Machi, Inashiki Gun, Ibaraki, 300-0332, Japan.
121 rdf:type schema:Organization
122 N7bb6ae93f224449485deccf91b56853b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
123 schema:name Proteome
124 rdf:type schema:DefinedTerm
125 N8742d528c5da41b5afc1053ba1bb8f2b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
126 schema:name Promoter Regions, Genetic
127 rdf:type schema:DefinedTerm
128 N9523da7fa64c4c7288b653f6bd3b36d1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
129 schema:name Transcription Factors
130 rdf:type schema:DefinedTerm
131 Na7a3f25058a34e13b45f6a67b4a0ec71 schema:name doi
132 schema:value 10.1038/nmeth768
133 rdf:type schema:PropertyValue
134 Nb4e93f7f64a1431dad0ae2baa906adda schema:issueNumber 7
135 rdf:type schema:PublicationIssue
136 Nbb9cf352e2e8424d8689c8ece04e567c rdf:first sg:person.01023710753.40
137 rdf:rest rdf:nil
138 Nc7dfcf446a7748eba0a6556f83988068 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
139 schema:name Genomics
140 rdf:type schema:DefinedTerm
141 Nca2e4ce67cab4df599e3225df9e52df3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
142 schema:name Systems Biology
143 rdf:type schema:DefinedTerm
144 Nda569ba7e256419eb5f157b7e212476e schema:name dimensions_id
145 schema:value pub.1006027429
146 rdf:type schema:PropertyValue
147 Ndf9ab1bf00644eb3bed64505a4fcda2e schema:name readcube_id
148 schema:value 1cb62284a2f4eee8b39a72821418cff94facba4a8f6c595e8fa928a717dd69ea
149 rdf:type schema:PropertyValue
150 Nf0ff39544f9f435eb71aa53cfb9d1ede schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
151 schema:name Transcription, Genetic
152 rdf:type schema:DefinedTerm
153 Nfde8300b633b41d7b39e4ab991d29527 schema:volumeNumber 2
154 rdf:type schema:PublicationVolume
155 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
156 schema:name Biological Sciences
157 rdf:type schema:DefinedTerm
158 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
159 schema:name Genetics
160 rdf:type schema:DefinedTerm
161 sg:journal.1033763 schema:issn 1548-7091
162 1548-7105
163 schema:name Nature Methods
164 rdf:type schema:Periodical
165 sg:person.01023710753.40 schema:affiliation https://www.grid.ac/institutes/grid.7597.c
166 schema:familyName Carninci
167 schema:givenName Piero
168 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01023710753.40
169 rdf:type schema:Person
170 sg:person.0662427634.38 schema:affiliation N7b227a0c469649508637cf3b1aa4e469
171 schema:familyName Harbers
172 schema:givenName Matthias
173 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0662427634.38
174 rdf:type schema:Person
175 sg:pub.10.1038/35057149 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046153445
176 https://doi.org/10.1038/35057149
177 rdf:type schema:CreativeWork
178 sg:pub.10.1038/76469 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028559169
179 https://doi.org/10.1038/76469
180 rdf:type schema:CreativeWork
181 sg:pub.10.1038/nature01266 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045627219
182 https://doi.org/10.1038/nature01266
183 rdf:type schema:CreativeWork
184 sg:pub.10.1038/nbt0502-508 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016616140
185 https://doi.org/10.1038/nbt0502-508
186 rdf:type schema:CreativeWork
187 sg:pub.10.1038/nbt964 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030931723
188 https://doi.org/10.1038/nbt964
189 rdf:type schema:CreativeWork
190 sg:pub.10.1038/nbt998 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026949774
191 https://doi.org/10.1038/nbt998
192 rdf:type schema:CreativeWork
193 sg:pub.10.1038/nmeth726 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030149986
194 https://doi.org/10.1038/nmeth726
195 rdf:type schema:CreativeWork
196 sg:pub.10.1038/nmeth733 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038506370
197 https://doi.org/10.1038/nmeth733
198 rdf:type schema:CreativeWork
199 https://app.dimensions.ai/details/publication/pub.1074672793 schema:CreativeWork
200 https://doi.org/10.1002/j.1460-2075.1986.tb04631.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1079514447
201 rdf:type schema:CreativeWork
202 https://doi.org/10.1006/geno.1996.0567 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019249665
203 rdf:type schema:CreativeWork
204 https://doi.org/10.1016/0378-1119(94)90802-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044144266
205 rdf:type schema:CreativeWork
206 https://doi.org/10.1016/j.bbrc.2004.07.200 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012298431
207 rdf:type schema:CreativeWork
208 https://doi.org/10.1016/j.tibtech.2003.11.002 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039600578
209 rdf:type schema:CreativeWork
210 https://doi.org/10.1016/j.tig.2003.09.014 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049684815
211 rdf:type schema:CreativeWork
212 https://doi.org/10.1016/s0014-5793(04)00018-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015721066
213 rdf:type schema:CreativeWork
214 https://doi.org/10.1016/s0076-6879(99)03004-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028617756
215 rdf:type schema:CreativeWork
216 https://doi.org/10.1016/s0378-1119(00)00557-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044851927
217 rdf:type schema:CreativeWork
218 https://doi.org/10.1073/pnas.0308384100 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005134437
219 rdf:type schema:CreativeWork
220 https://doi.org/10.1073/pnas.0403514101 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013107285
221 rdf:type schema:CreativeWork
222 https://doi.org/10.1073/pnas.0407387101 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026102531
223 rdf:type schema:CreativeWork
224 https://doi.org/10.1073/pnas.202610899 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050518611
225 rdf:type schema:CreativeWork
226 https://doi.org/10.1073/pnas.2136655100 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028529038
227 rdf:type schema:CreativeWork
228 https://doi.org/10.1073/pnas.2536670100 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032730078
229 rdf:type schema:CreativeWork
230 https://doi.org/10.1093/bioinformatics/16.11.953 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045857704
231 rdf:type schema:CreativeWork
232 https://doi.org/10.1093/nar/25.17.3389 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047265454
233 rdf:type schema:CreativeWork
234 https://doi.org/10.1093/nar/30.1.207 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005297170
235 rdf:type schema:CreativeWork
236 https://doi.org/10.1093/nar/gkg763 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019401433
237 rdf:type schema:CreativeWork
238 https://doi.org/10.1093/nar/gkh937 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030573947
239 rdf:type schema:CreativeWork
240 https://doi.org/10.1093/nar/gki020 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035717041
241 rdf:type schema:CreativeWork
242 https://doi.org/10.1093/nar/gki085 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009501697
243 rdf:type schema:CreativeWork
244 https://doi.org/10.1101/gad.1256904 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031360678
245 rdf:type schema:CreativeWork
246 https://doi.org/10.1101/gr.10.7.1051 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017945935
247 rdf:type schema:CreativeWork
248 https://doi.org/10.1101/gr.1119703 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043471471
249 rdf:type schema:CreativeWork
250 https://doi.org/10.1101/gr.1414204 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045727851
251 rdf:type schema:CreativeWork
252 https://doi.org/10.1101/gr.145100 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017491574
253 rdf:type schema:CreativeWork
254 https://doi.org/10.1101/gr.2094104 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050487471
255 rdf:type schema:CreativeWork
256 https://doi.org/10.1101/gr.2596504 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044936424
257 rdf:type schema:CreativeWork
258 https://doi.org/10.1101/gr.2769804 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037481214
259 rdf:type schema:CreativeWork
260 https://doi.org/10.1101/gr.873003 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002115475
261 rdf:type schema:CreativeWork
262 https://doi.org/10.1111/j.1462-5822.2004.00478.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1027457227
263 rdf:type schema:CreativeWork
264 https://doi.org/10.1126/science.1075090 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001953109
265 rdf:type schema:CreativeWork
266 https://doi.org/10.1126/science.1103388 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042123507
267 rdf:type schema:CreativeWork
268 https://doi.org/10.1126/science.1108625 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046921907
269 rdf:type schema:CreativeWork
270 https://doi.org/10.1126/science.270.5235.484 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062551479
271 rdf:type schema:CreativeWork
272 https://doi.org/10.1126/science.280.5366.1077 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062561068
273 rdf:type schema:CreativeWork
274 https://doi.org/10.1126/science.290.5499.2144 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062572479
275 rdf:type schema:CreativeWork
276 https://doi.org/10.1126/science.292.5518.929 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004753512
277 rdf:type schema:CreativeWork
278 https://doi.org/10.1126/science.306.5696.630 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062586440
279 rdf:type schema:CreativeWork
280 https://doi.org/10.1128/mcb.1.2.179 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009728814
281 rdf:type schema:CreativeWork
282 https://doi.org/10.1128/mcb.15.6.3363 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053537361
283 rdf:type schema:CreativeWork
284 https://doi.org/10.1146/annurev.biochem.72.121801.161720 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045905529
285 rdf:type schema:CreativeWork
286 https://doi.org/10.1146/annurev.genom.2.1.343 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019815147
287 rdf:type schema:CreativeWork
288 https://doi.org/10.1152/physiolgenomics.2001.6.2.57 schema:sameAs https://app.dimensions.ai/details/publication/pub.1074851182
289 rdf:type schema:CreativeWork
290 https://doi.org/10.2144/01315st04 schema:sameAs https://app.dimensions.ai/details/publication/pub.1074960954
291 rdf:type schema:CreativeWork
292 https://www.grid.ac/institutes/grid.7597.c schema:alternateName RIKEN
293 schema:name Genome Science Laboratory, RIKEN, Wako main campus, Hirosawa 2-1 Wako, Japan.
294 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...