Identification of functional SNPs in the 5-prime flanking sequences of human genes View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2005-12

AUTHORS

Salim Mottagui-Tabar, Mohammad A Faghihi, Yosuke Mizuno, Pär G Engström, Boris Lenhard, Wyeth W Wasserman, Claes Wahlestedt

ABSTRACT

BACKGROUND: Over 4 million single nucleotide polymorphisms (SNPs) are currently reported to exist within the human genome. Only a small fraction of these SNPs alter gene function or expression, and therefore might be associated with a cell phenotype. These functional SNPs are consequently important in understanding human health. Information related to functional SNPs in candidate disease genes is critical for cost effective genetic association studies, which attempt to understand the genetics of complex diseases like diabetes, Alzheimer's, etc. Robust methods for the identification of functional SNPs are therefore crucial. We report one such experimental approach. RESULTS: Sequence conserved between mouse and human genomes, within 5 kilobases of the 5-prime end of 176 GPCR genes, were screened for SNPs. Sequences flanking these SNPs were scored for transcription factor binding sites. Allelic pairs resulting in a significant score difference were predicted to influence the binding of transcription factors (TFs). Ten such SNPs were selected for mobility shift assays (EMSA), resulting in 7 of them exhibiting a reproducible shift. The full-length promoter regions with 4 of the 7 SNPs were cloned in a Luciferase based plasmid reporter system. Two out of the 4 SNPs exhibited differential promoter activity in several human cell lines. CONCLUSIONS: We propose a method for effective selection of functional, regulatory SNPs that are located in evolutionary conserved 5-prime flanking regions (5'-FR) regions of human genes and influence the activity of the transcriptional regulatory region. Some SNPs behave differently in different cell types. More... »

PAGES

18

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2164-6-18

DOI

http://dx.doi.org/10.1186/1471-2164-6-18

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1047377016

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/15717931


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": "Algorithms", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Alleles", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Animals", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Binding Sites", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Cell Line", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Chromosome Mapping", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Conserved Sequence", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Evolution, Molecular", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gene Expression Regulation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genome, Human", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Humans", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Luciferases", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Mice", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Models, Genetic", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Molecular Sequence Data", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Oligonucleotides", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Phenotype", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Plasmids", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Polymorphism, Restriction Fragment Length", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Polymorphism, Single Nucleotide", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Promoter Regions, Genetic", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Protein Binding", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sequence Analysis, DNA", 
        "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": {
          "alternateName": "Karolinska Institute", 
          "id": "https://www.grid.ac/institutes/grid.4714.6", 
          "name": [
            "Center for Genomics and Bioinformatics, Karolinska Institutet, SE-17177, Stockholm, Sweden"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Mottagui-Tabar", 
        "givenName": "Salim", 
        "id": "sg:person.01061514124.55", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01061514124.55"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Karolinska Institute", 
          "id": "https://www.grid.ac/institutes/grid.4714.6", 
          "name": [
            "Center for Genomics and Bioinformatics, Karolinska Institutet, SE-17177, Stockholm, Sweden"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Faghihi", 
        "givenName": "Mohammad A", 
        "id": "sg:person.0765270443.33", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0765270443.33"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Karolinska Institute", 
          "id": "https://www.grid.ac/institutes/grid.4714.6", 
          "name": [
            "Center for Genomics and Bioinformatics, Karolinska Institutet, SE-17177, Stockholm, Sweden"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Mizuno", 
        "givenName": "Yosuke", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Karolinska Institute", 
          "id": "https://www.grid.ac/institutes/grid.4714.6", 
          "name": [
            "Center for Genomics and Bioinformatics, Karolinska Institutet, SE-17177, Stockholm, Sweden"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Engstr\u00f6m", 
        "givenName": "P\u00e4r G", 
        "id": "sg:person.01232124755.17", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01232124755.17"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Karolinska Institute", 
          "id": "https://www.grid.ac/institutes/grid.4714.6", 
          "name": [
            "Center for Genomics and Bioinformatics, Karolinska Institutet, SE-17177, Stockholm, Sweden"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Lenhard", 
        "givenName": "Boris", 
        "id": "sg:person.01064443570.02", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01064443570.02"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of British Columbia", 
          "id": "https://www.grid.ac/institutes/grid.17091.3e", 
          "name": [
            "Centre for Molecular Medicine and Therapeutics, University of British Columbia, V5Z 4H4, Vancouver, BC, Canada"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Wasserman", 
        "givenName": "Wyeth W", 
        "id": "sg:person.01164162122.26", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01164162122.26"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Karolinska Institute", 
          "id": "https://www.grid.ac/institutes/grid.4714.6", 
          "name": [
            "Center for Genomics and Bioinformatics, Karolinska Institutet, SE-17177, Stockholm, Sweden"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Wahlestedt", 
        "givenName": "Claes", 
        "id": "sg:person.010066724757.69", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010066724757.69"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1016/s0959-440x(97)80058-9", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001488689"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/29.1.308", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005817660"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.229202", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006260064"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35052548", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006744313", 
          "https://doi.org/10.1038/35052548"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35052548", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006744313", 
          "https://doi.org/10.1038/35052548"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkg112", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006846104"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/10290", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1008973203", 
          "https://doi.org/10.1038/10290"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/10290", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1008973203", 
          "https://doi.org/10.1038/10290"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0014-5793(02)02564-4", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011794105"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkg129", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012203647"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1161/hq1101.098229", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016634623"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/hmg/10.6.591", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018892969"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1006/jmbi.1996.0760", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1020032613"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1146/annurev.pharmtox.41.1.593", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022015548"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.180601", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022605725"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/28.1.356", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026974525"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1475-4924-2-13", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1029375403", 
          "https://doi.org/10.1186/1475-4924-2-13"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0168-9525(01)02344-7", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030156670"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkh012", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031148109"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0168-9525(00)01988-0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036102903"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/16.1.16", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036725436"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/mcb.16.1.437", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037198881"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gki138", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043230895"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkf493", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043756780"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/9780470110607.ch10", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044416316"
        ], 
        "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/10.1126/science.288.5463.136", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045941060"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/18.8.1135", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046379219"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.809403", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047191638"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.199801", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049065605"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1006/jmbi.2001.4510", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051365993"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1208/ps030322", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051876161", 
          "https://doi.org/10.1208/ps030322"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.287.5461.2204", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062568860"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.2174/0929867003374534", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1069159677"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1074670453", 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2005-12", 
    "datePublishedReg": "2005-12-01", 
    "description": "BACKGROUND: Over 4 million single nucleotide polymorphisms (SNPs) are currently reported to exist within the human genome. Only a small fraction of these SNPs alter gene function or expression, and therefore might be associated with a cell phenotype. These functional SNPs are consequently important in understanding human health. Information related to functional SNPs in candidate disease genes is critical for cost effective genetic association studies, which attempt to understand the genetics of complex diseases like diabetes, Alzheimer's, etc. Robust methods for the identification of functional SNPs are therefore crucial. We report one such experimental approach.\nRESULTS: Sequence conserved between mouse and human genomes, within 5 kilobases of the 5-prime end of 176 GPCR genes, were screened for SNPs. Sequences flanking these SNPs were scored for transcription factor binding sites. Allelic pairs resulting in a significant score difference were predicted to influence the binding of transcription factors (TFs). Ten such SNPs were selected for mobility shift assays (EMSA), resulting in 7 of them exhibiting a reproducible shift. The full-length promoter regions with 4 of the 7 SNPs were cloned in a Luciferase based plasmid reporter system. Two out of the 4 SNPs exhibited differential promoter activity in several human cell lines.\nCONCLUSIONS: We propose a method for effective selection of functional, regulatory SNPs that are located in evolutionary conserved 5-prime flanking regions (5'-FR) regions of human genes and influence the activity of the transcriptional regulatory region. Some SNPs behave differently in different cell types.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1186/1471-2164-6-18", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isPartOf": [
      {
        "id": "sg:journal.1023790", 
        "issn": [
          "1471-2164"
        ], 
        "name": "BMC Genomics", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "6"
      }
    ], 
    "name": "Identification of functional SNPs in the 5-prime flanking sequences of human genes", 
    "pagination": "18", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "e1b06d866eed71c70c7a16cbb539532b3e7e8ad10df6a79fe53fa2c976a472be"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "15717931"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "100965258"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/1471-2164-6-18"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1047377016"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/1471-2164-6-18", 
      "https://app.dimensions.ai/details/publication/pub.1047377016"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T19:56", 
    "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_8681_00000507.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://link.springer.com/10.1186%2F1471-2164-6-18"
  }
]
 

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.10.1186/1471-2164-6-18'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-6-18'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-6-18'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-6-18'


 

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

315 TRIPLES      21 PREDICATES      87 URIs      46 LITERALS      34 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/1471-2164-6-18 schema:about N00e3ddeda900402e9d66839c58aec204
2 N07d4bce5557448fda3d434f49ce6b6e2
3 N124abd42c8ff4de5a226c3809127e317
4 N1b59fd58447f4c3c97942f3902cbb70f
5 N2deb78de40df473a944f6f602e9cbce1
6 N31712648cf1c40cc93edba9a9ef85f99
7 N36186c603d3b46079151cf703de9a835
8 N3f0cde919ee84e72853427b3b2b02d7f
9 N40dd2f4cea864dc7bd06067cd69fda83
10 N4a33a39baea244418587f598b438c42e
11 N4a6270c589314fb3a25708c1fb66d106
12 N5578051e7fe1465ba6424b4f714ce6c5
13 N59f79ac454704d89839c6116c0fd0a33
14 N5bfdeac623344b248988968bc3b19462
15 N626c8e072a244c8192ff568bef96ca65
16 N69cbaa1f82854138b3388d1eda352407
17 N8324202529b14e81be7feb6e09ddd9f1
18 N8330caabacde4a3fb6e6b3a71a35cfe5
19 N85e8e9f0cb2b4088b5fcafd943201f2e
20 Na1607cc2c1df491c839aebec3c187243
21 Nb1abf405e4ac485b8f949f9f9e1678d7
22 Ncdda0e7a2c7844f5853da0c4fbb19e03
23 Ncdf8e25a61e54df3b6281b7235f8d904
24 Nee975d8873244bed99b06de96219cff5
25 Nf88ac5d09bfe419f8063318e74f324e3
26 anzsrc-for:06
27 anzsrc-for:0604
28 schema:author N81166c4cd1c344d3b0c156639c5150bd
29 schema:citation sg:pub.10.1038/10290
30 sg:pub.10.1038/35052548
31 sg:pub.10.1038/nature01266
32 sg:pub.10.1186/1475-4924-2-13
33 sg:pub.10.1208/ps030322
34 https://app.dimensions.ai/details/publication/pub.1074670453
35 https://doi.org/10.1002/9780470110607.ch10
36 https://doi.org/10.1006/jmbi.1996.0760
37 https://doi.org/10.1006/jmbi.2001.4510
38 https://doi.org/10.1016/s0014-5793(02)02564-4
39 https://doi.org/10.1016/s0168-9525(00)01988-0
40 https://doi.org/10.1016/s0168-9525(01)02344-7
41 https://doi.org/10.1016/s0959-440x(97)80058-9
42 https://doi.org/10.1093/bioinformatics/16.1.16
43 https://doi.org/10.1093/bioinformatics/18.8.1135
44 https://doi.org/10.1093/hmg/10.6.591
45 https://doi.org/10.1093/nar/28.1.356
46 https://doi.org/10.1093/nar/29.1.308
47 https://doi.org/10.1093/nar/gkf493
48 https://doi.org/10.1093/nar/gkg112
49 https://doi.org/10.1093/nar/gkg129
50 https://doi.org/10.1093/nar/gkh012
51 https://doi.org/10.1093/nar/gki138
52 https://doi.org/10.1101/gr.180601
53 https://doi.org/10.1101/gr.199801
54 https://doi.org/10.1101/gr.229202
55 https://doi.org/10.1101/gr.809403
56 https://doi.org/10.1126/science.287.5461.2204
57 https://doi.org/10.1126/science.288.5463.136
58 https://doi.org/10.1128/mcb.16.1.437
59 https://doi.org/10.1146/annurev.pharmtox.41.1.593
60 https://doi.org/10.1161/hq1101.098229
61 https://doi.org/10.2174/0929867003374534
62 schema:datePublished 2005-12
63 schema:datePublishedReg 2005-12-01
64 schema:description BACKGROUND: Over 4 million single nucleotide polymorphisms (SNPs) are currently reported to exist within the human genome. Only a small fraction of these SNPs alter gene function or expression, and therefore might be associated with a cell phenotype. These functional SNPs are consequently important in understanding human health. Information related to functional SNPs in candidate disease genes is critical for cost effective genetic association studies, which attempt to understand the genetics of complex diseases like diabetes, Alzheimer's, etc. Robust methods for the identification of functional SNPs are therefore crucial. We report one such experimental approach. RESULTS: Sequence conserved between mouse and human genomes, within 5 kilobases of the 5-prime end of 176 GPCR genes, were screened for SNPs. Sequences flanking these SNPs were scored for transcription factor binding sites. Allelic pairs resulting in a significant score difference were predicted to influence the binding of transcription factors (TFs). Ten such SNPs were selected for mobility shift assays (EMSA), resulting in 7 of them exhibiting a reproducible shift. The full-length promoter regions with 4 of the 7 SNPs were cloned in a Luciferase based plasmid reporter system. Two out of the 4 SNPs exhibited differential promoter activity in several human cell lines. CONCLUSIONS: We propose a method for effective selection of functional, regulatory SNPs that are located in evolutionary conserved 5-prime flanking regions (5'-FR) regions of human genes and influence the activity of the transcriptional regulatory region. Some SNPs behave differently in different cell types.
65 schema:genre research_article
66 schema:inLanguage en
67 schema:isAccessibleForFree true
68 schema:isPartOf N290cdc16fc3141ce967bcd1c919f86ec
69 Nd329d0b8704f49f3aabc9c8341a18863
70 sg:journal.1023790
71 schema:name Identification of functional SNPs in the 5-prime flanking sequences of human genes
72 schema:pagination 18
73 schema:productId N3880108d15f94f999796b89ba1adbb75
74 N4ed1613f38a748a9a5f9b2ffa9dfe0dc
75 Ncdc1e991945b4351864a99bd79b647fb
76 Nf6df1e6c11cf40848528a2e1ecade8ac
77 Nf89d82032e9442b283c0332a5ae3580e
78 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047377016
79 https://doi.org/10.1186/1471-2164-6-18
80 schema:sdDatePublished 2019-04-10T19:56
81 schema:sdLicense https://scigraph.springernature.com/explorer/license/
82 schema:sdPublisher Nb9545c0836b54b99bd0e60de95e65569
83 schema:url http://link.springer.com/10.1186%2F1471-2164-6-18
84 sgo:license sg:explorer/license/
85 sgo:sdDataset articles
86 rdf:type schema:ScholarlyArticle
87 N00e3ddeda900402e9d66839c58aec204 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
88 schema:name Cell Line
89 rdf:type schema:DefinedTerm
90 N07d4bce5557448fda3d434f49ce6b6e2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
91 schema:name Oligonucleotides
92 rdf:type schema:DefinedTerm
93 N124abd42c8ff4de5a226c3809127e317 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
94 schema:name Evolution, Molecular
95 rdf:type schema:DefinedTerm
96 N13313cefd99f46cfa713dc332e953d3a rdf:first sg:person.010066724757.69
97 rdf:rest rdf:nil
98 N1b59fd58447f4c3c97942f3902cbb70f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
99 schema:name Chromosome Mapping
100 rdf:type schema:DefinedTerm
101 N217028564fc84509b37048c5ea39e095 rdf:first N4f1920235022409aac3973915f28b2a7
102 rdf:rest N24d0ddd74d174bd1bf5c979ab8619977
103 N24d0ddd74d174bd1bf5c979ab8619977 rdf:first sg:person.01232124755.17
104 rdf:rest N6abc7dba214d471b9dbba24777919ffe
105 N290cdc16fc3141ce967bcd1c919f86ec schema:volumeNumber 6
106 rdf:type schema:PublicationVolume
107 N2deb78de40df473a944f6f602e9cbce1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
108 schema:name Models, Genetic
109 rdf:type schema:DefinedTerm
110 N31712648cf1c40cc93edba9a9ef85f99 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
111 schema:name Genome, Human
112 rdf:type schema:DefinedTerm
113 N36186c603d3b46079151cf703de9a835 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
114 schema:name Algorithms
115 rdf:type schema:DefinedTerm
116 N3880108d15f94f999796b89ba1adbb75 schema:name nlm_unique_id
117 schema:value 100965258
118 rdf:type schema:PropertyValue
119 N3f0cde919ee84e72853427b3b2b02d7f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
120 schema:name Luciferases
121 rdf:type schema:DefinedTerm
122 N40dd2f4cea864dc7bd06067cd69fda83 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
123 schema:name Phenotype
124 rdf:type schema:DefinedTerm
125 N4a33a39baea244418587f598b438c42e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
126 schema:name Humans
127 rdf:type schema:DefinedTerm
128 N4a6270c589314fb3a25708c1fb66d106 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
129 schema:name Molecular Sequence Data
130 rdf:type schema:DefinedTerm
131 N4ed1613f38a748a9a5f9b2ffa9dfe0dc schema:name pubmed_id
132 schema:value 15717931
133 rdf:type schema:PropertyValue
134 N4f1920235022409aac3973915f28b2a7 schema:affiliation https://www.grid.ac/institutes/grid.4714.6
135 schema:familyName Mizuno
136 schema:givenName Yosuke
137 rdf:type schema:Person
138 N5578051e7fe1465ba6424b4f714ce6c5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
139 schema:name Alleles
140 rdf:type schema:DefinedTerm
141 N59f79ac454704d89839c6116c0fd0a33 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
142 schema:name Polymorphism, Single Nucleotide
143 rdf:type schema:DefinedTerm
144 N5bfdeac623344b248988968bc3b19462 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
145 schema:name Mice
146 rdf:type schema:DefinedTerm
147 N626c8e072a244c8192ff568bef96ca65 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
148 schema:name Sequence Analysis, DNA
149 rdf:type schema:DefinedTerm
150 N69cbaa1f82854138b3388d1eda352407 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
151 schema:name Plasmids
152 rdf:type schema:DefinedTerm
153 N6abc7dba214d471b9dbba24777919ffe rdf:first sg:person.01064443570.02
154 rdf:rest N9cc42d93860d4db0bac80ef4005f8631
155 N81166c4cd1c344d3b0c156639c5150bd rdf:first sg:person.01061514124.55
156 rdf:rest Nfe318da0e52a4b55b86e81a76de4fa9e
157 N8324202529b14e81be7feb6e09ddd9f1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
158 schema:name Conserved Sequence
159 rdf:type schema:DefinedTerm
160 N8330caabacde4a3fb6e6b3a71a35cfe5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
161 schema:name Gene Expression Regulation
162 rdf:type schema:DefinedTerm
163 N85e8e9f0cb2b4088b5fcafd943201f2e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
164 schema:name Promoter Regions, Genetic
165 rdf:type schema:DefinedTerm
166 N9cc42d93860d4db0bac80ef4005f8631 rdf:first sg:person.01164162122.26
167 rdf:rest N13313cefd99f46cfa713dc332e953d3a
168 Na1607cc2c1df491c839aebec3c187243 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
169 schema:name Animals
170 rdf:type schema:DefinedTerm
171 Nb1abf405e4ac485b8f949f9f9e1678d7 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
172 schema:name Polymorphism, Restriction Fragment Length
173 rdf:type schema:DefinedTerm
174 Nb9545c0836b54b99bd0e60de95e65569 schema:name Springer Nature - SN SciGraph project
175 rdf:type schema:Organization
176 Ncdc1e991945b4351864a99bd79b647fb schema:name dimensions_id
177 schema:value pub.1047377016
178 rdf:type schema:PropertyValue
179 Ncdda0e7a2c7844f5853da0c4fbb19e03 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
180 schema:name Protein Binding
181 rdf:type schema:DefinedTerm
182 Ncdf8e25a61e54df3b6281b7235f8d904 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
183 schema:name Binding Sites
184 rdf:type schema:DefinedTerm
185 Nd329d0b8704f49f3aabc9c8341a18863 schema:issueNumber 1
186 rdf:type schema:PublicationIssue
187 Nee975d8873244bed99b06de96219cff5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
188 schema:name Transcription Factors
189 rdf:type schema:DefinedTerm
190 Nf6df1e6c11cf40848528a2e1ecade8ac schema:name doi
191 schema:value 10.1186/1471-2164-6-18
192 rdf:type schema:PropertyValue
193 Nf88ac5d09bfe419f8063318e74f324e3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
194 schema:name Transcription, Genetic
195 rdf:type schema:DefinedTerm
196 Nf89d82032e9442b283c0332a5ae3580e schema:name readcube_id
197 schema:value e1b06d866eed71c70c7a16cbb539532b3e7e8ad10df6a79fe53fa2c976a472be
198 rdf:type schema:PropertyValue
199 Nfe318da0e52a4b55b86e81a76de4fa9e rdf:first sg:person.0765270443.33
200 rdf:rest N217028564fc84509b37048c5ea39e095
201 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
202 schema:name Biological Sciences
203 rdf:type schema:DefinedTerm
204 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
205 schema:name Genetics
206 rdf:type schema:DefinedTerm
207 sg:journal.1023790 schema:issn 1471-2164
208 schema:name BMC Genomics
209 rdf:type schema:Periodical
210 sg:person.010066724757.69 schema:affiliation https://www.grid.ac/institutes/grid.4714.6
211 schema:familyName Wahlestedt
212 schema:givenName Claes
213 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010066724757.69
214 rdf:type schema:Person
215 sg:person.01061514124.55 schema:affiliation https://www.grid.ac/institutes/grid.4714.6
216 schema:familyName Mottagui-Tabar
217 schema:givenName Salim
218 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01061514124.55
219 rdf:type schema:Person
220 sg:person.01064443570.02 schema:affiliation https://www.grid.ac/institutes/grid.4714.6
221 schema:familyName Lenhard
222 schema:givenName Boris
223 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01064443570.02
224 rdf:type schema:Person
225 sg:person.01164162122.26 schema:affiliation https://www.grid.ac/institutes/grid.17091.3e
226 schema:familyName Wasserman
227 schema:givenName Wyeth W
228 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01164162122.26
229 rdf:type schema:Person
230 sg:person.01232124755.17 schema:affiliation https://www.grid.ac/institutes/grid.4714.6
231 schema:familyName Engström
232 schema:givenName Pär G
233 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01232124755.17
234 rdf:type schema:Person
235 sg:person.0765270443.33 schema:affiliation https://www.grid.ac/institutes/grid.4714.6
236 schema:familyName Faghihi
237 schema:givenName Mohammad A
238 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0765270443.33
239 rdf:type schema:Person
240 sg:pub.10.1038/10290 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008973203
241 https://doi.org/10.1038/10290
242 rdf:type schema:CreativeWork
243 sg:pub.10.1038/35052548 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006744313
244 https://doi.org/10.1038/35052548
245 rdf:type schema:CreativeWork
246 sg:pub.10.1038/nature01266 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045627219
247 https://doi.org/10.1038/nature01266
248 rdf:type schema:CreativeWork
249 sg:pub.10.1186/1475-4924-2-13 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029375403
250 https://doi.org/10.1186/1475-4924-2-13
251 rdf:type schema:CreativeWork
252 sg:pub.10.1208/ps030322 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051876161
253 https://doi.org/10.1208/ps030322
254 rdf:type schema:CreativeWork
255 https://app.dimensions.ai/details/publication/pub.1074670453 schema:CreativeWork
256 https://doi.org/10.1002/9780470110607.ch10 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044416316
257 rdf:type schema:CreativeWork
258 https://doi.org/10.1006/jmbi.1996.0760 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020032613
259 rdf:type schema:CreativeWork
260 https://doi.org/10.1006/jmbi.2001.4510 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051365993
261 rdf:type schema:CreativeWork
262 https://doi.org/10.1016/s0014-5793(02)02564-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011794105
263 rdf:type schema:CreativeWork
264 https://doi.org/10.1016/s0168-9525(00)01988-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036102903
265 rdf:type schema:CreativeWork
266 https://doi.org/10.1016/s0168-9525(01)02344-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030156670
267 rdf:type schema:CreativeWork
268 https://doi.org/10.1016/s0959-440x(97)80058-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001488689
269 rdf:type schema:CreativeWork
270 https://doi.org/10.1093/bioinformatics/16.1.16 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036725436
271 rdf:type schema:CreativeWork
272 https://doi.org/10.1093/bioinformatics/18.8.1135 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046379219
273 rdf:type schema:CreativeWork
274 https://doi.org/10.1093/hmg/10.6.591 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018892969
275 rdf:type schema:CreativeWork
276 https://doi.org/10.1093/nar/28.1.356 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026974525
277 rdf:type schema:CreativeWork
278 https://doi.org/10.1093/nar/29.1.308 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005817660
279 rdf:type schema:CreativeWork
280 https://doi.org/10.1093/nar/gkf493 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043756780
281 rdf:type schema:CreativeWork
282 https://doi.org/10.1093/nar/gkg112 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006846104
283 rdf:type schema:CreativeWork
284 https://doi.org/10.1093/nar/gkg129 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012203647
285 rdf:type schema:CreativeWork
286 https://doi.org/10.1093/nar/gkh012 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031148109
287 rdf:type schema:CreativeWork
288 https://doi.org/10.1093/nar/gki138 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043230895
289 rdf:type schema:CreativeWork
290 https://doi.org/10.1101/gr.180601 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022605725
291 rdf:type schema:CreativeWork
292 https://doi.org/10.1101/gr.199801 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049065605
293 rdf:type schema:CreativeWork
294 https://doi.org/10.1101/gr.229202 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006260064
295 rdf:type schema:CreativeWork
296 https://doi.org/10.1101/gr.809403 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047191638
297 rdf:type schema:CreativeWork
298 https://doi.org/10.1126/science.287.5461.2204 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062568860
299 rdf:type schema:CreativeWork
300 https://doi.org/10.1126/science.288.5463.136 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045941060
301 rdf:type schema:CreativeWork
302 https://doi.org/10.1128/mcb.16.1.437 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037198881
303 rdf:type schema:CreativeWork
304 https://doi.org/10.1146/annurev.pharmtox.41.1.593 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022015548
305 rdf:type schema:CreativeWork
306 https://doi.org/10.1161/hq1101.098229 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016634623
307 rdf:type schema:CreativeWork
308 https://doi.org/10.2174/0929867003374534 schema:sameAs https://app.dimensions.ai/details/publication/pub.1069159677
309 rdf:type schema:CreativeWork
310 https://www.grid.ac/institutes/grid.17091.3e schema:alternateName University of British Columbia
311 schema:name Centre for Molecular Medicine and Therapeutics, University of British Columbia, V5Z 4H4, Vancouver, BC, Canada
312 rdf:type schema:Organization
313 https://www.grid.ac/institutes/grid.4714.6 schema:alternateName Karolinska Institute
314 schema:name Center for Genomics and Bioinformatics, Karolinska Institutet, SE-17177, Stockholm, Sweden
315 rdf:type schema:Organization
 




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


...