DOI: 10.1093/bioinformatics/btk031. SUSPECTS: enabling fast and effective prioritization of positional candidates

SUSPECTS: enabling fast and effective prioritization of positional candidates

10.1093/bioinformatics/btk031

Crossref journal-article

Oxford University Press (OUP)

Bioinformatics (286)

Abstract

Abstract Summary: SUSPECTS is a web-based server which combines annotation and sequence-based approaches to prioritize disease candidate genes in large regions of interest. It uses multiple lines of evidence to rank genes quickly and effectively while limiting the effect of annotation bias to significantly improve performance. Availability: SUSPECTS is freely available at Contact: euan.adie@ed.ac.uk Supplementary information: A quick-start guide in Macromedia Flash format is available at and Excel spreadsheets detailing the comparative performance of the software are included as Supplementary material.

Bibliography

Adie, E. A., Adams, R. R., Evans, K. L., Porteous, D. J., & Pickard, B. S. (2006). SUSPECTS: enabling fast and effective prioritization of positional candidates. Bioinformatics, 22(6), 773â774.

Authors 5

E. A. Adie (first)
R. R. Adams (additional)
K. L. Evans (additional)
D. J. Porteous (additional)
B. S. Pickard (additional)

References 13 Referenced 193

10.1186/1471-2105-6-55 / BMC Bioinformatics / Speeding disease gene discovery by sequence based candidate prioritization by Adie (2005)
10.1038/ng0504-431 / Nat. Genet. / The Genetic Association Database by Becker (2004)
10.1093/nar/26.1.285 / Nucleic Acids Res. / The human gene mutation database by Cooper (1998)
10.1093/bioinformatics/18.suppl_2.S110 / Bioinformatics / A similarity-based method for genome-wide prediction of disease-relevant human genes by Freudenberg (2002)
10.1093/nar/30.1.52 / Nucleic Acids Res. / Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders by Hamosh (2002)
10.1093/nar/gkh605 / Nucleic Acids Res. / Genome-wide identification of genes likely to be involved in human genetic disease by Lopez-Bigas (2004)
10.1093/bioinformatics/btg153 / Bioinformatics / Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation by Lord (2003)
10.1186/gb-2003-4-10-119 / Genome Biol. / New methods for finding disease-susceptibility genes: impact and potential by McCarthy (2003)
10.1038/ng895 / Nat. Genet. / Association of genes to genetically inherited diseases using data mining by Perez-Iratxeta (2002)
10.1073/pnas.012025199 / Proc. Natl Acad. Sci. USA / Large-scale analysis of the human and mouse transcriptomes by Su (2002)
10.1093/nar/gki296 / Nucleic Acids Res. / Integration of text- and data-mining using ontologies successfully selects disease gene candidates by Tiffin (2005)
10.1186/gb-2003-4-11-r75 / Genome Biol. / POCUS: mining genomic sequence annotation to predict disease genes by Turner (2003)
10.1038/sj.ejhg.5200918 / Eur. J. Hum. Genet. / A new web-based data mining tool for the identification of candidate genes for human genetic disorders by Van Driel (2003)

Dates

Type	When
Created	19 years, 7 months ago (Jan. 19, 2006, 8:47 p.m.)
Deposited	2 years, 7 months ago (Jan. 24, 2023, 4:32 a.m.)
Indexed	9 months, 1 week ago (Nov. 19, 2024, 10:57 a.m.)
Issued	19 years, 7 months ago (Jan. 19, 2006)
Published	19 years, 7 months ago (Jan. 19, 2006)
Published Online	19 years, 7 months ago (Jan. 19, 2006)
Published Print	19 years, 5 months ago (March 15, 2006)

Funders 0

None

BibTeX

@article{Adie_2006, title={SUSPECTS: enabling fast and effective prioritization of positional candidates}, volume={22}, ISSN={1367-4803}, url={http://dx.doi.org/10.1093/bioinformatics/btk031}, DOI={10.1093/bioinformatics/btk031}, number={6}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Adie, E. A. and Adams, R. R. and Evans, K. L. and Porteous, D. J. and Pickard, B. S.}, year={2006}, month=jan, pages={773–774} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2024,
        11,
        19
      ]
    ],
    "date-time": "2024-11-19T15:57:21Z",
    "timestamp": 1732031841711
  },
  "reference-count": 13,
  "publisher": "Oxford University Press (OUP)",
  "issue": "6",
  "content-domain": {
    "domain": [],
    "crossmark-restriction": false
  },
  "published-print": {
    "date-parts": [
      [
        2006,
        3,
        15
      ]
    ]
  },
  "abstract": "<jats:title>Abstract</jats:title>\n               <jats:p>Summary: SUSPECTS is a web-based server which combines annotation and sequence-based approaches to prioritize disease candidate genes in large regions of interest. It uses multiple lines of evidence to rank genes quickly and effectively while limiting the effect of annotation bias to significantly improve performance.</jats:p>\n               <jats:p>Availability: SUSPECTS is freely available at</jats:p>\n               <jats:p>Contact: \u00a0euan.adie@ed.ac.uk</jats:p>\n               <jats:p>Supplementary information: A quick-start guide in Macromedia Flash format is available at and Excel spreadsheets detailing the comparative performance of the software are included as Supplementary material.</jats:p>",
  "DOI": "10.1093/bioinformatics/btk031",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2006,
        1,
        20
      ]
    ],
    "date-time": "2006-01-20T01:47:41Z",
    "timestamp": 1137721661000
  },
  "page": "773-774",
  "source": "Crossref",
  "is-referenced-by-count": 193,
  "title": "SUSPECTS: enabling fast and effective prioritization of positional candidates",
  "prefix": "10.1093",
  "volume": "22",
  "author": [
    {
      "given": "E. A.",
      "family": "Adie",
      "sequence": "first",
      "affiliation": [
        {
          "name": "Medical Genetics Section, School of Molecular and Clinical Medicine, University of Edinburgh EH4 2XU \u00a0 UK"
        }
      ]
    },
    {
      "given": "R. R.",
      "family": "Adams",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Medical Genetics Section, School of Molecular and Clinical Medicine, University of Edinburgh EH4 2XU \u00a0 UK"
        }
      ]
    },
    {
      "given": "K. L.",
      "family": "Evans",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Medical Genetics Section, School of Molecular and Clinical Medicine, University of Edinburgh EH4 2XU \u00a0 UK"
        }
      ]
    },
    {
      "given": "D. J.",
      "family": "Porteous",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Medical Genetics Section, School of Molecular and Clinical Medicine, University of Edinburgh EH4 2XU \u00a0 UK"
        }
      ]
    },
    {
      "given": "B. S.",
      "family": "Pickard",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Medical Genetics Section, School of Molecular and Clinical Medicine, University of Edinburgh EH4 2XU \u00a0 UK"
        }
      ]
    }
  ],
  "member": "286",
  "published-online": {
    "date-parts": [
      [
        2006,
        1,
        19
      ]
    ]
  },
  "reference": [
    {
      "key": "2023012408532753900_b1",
      "doi-asserted-by": "crossref",
      "first-page": "55",
      "DOI": "10.1186/1471-2105-6-55",
      "article-title": "Speeding disease gene discovery by sequence based candidate prioritization",
      "volume": "6",
      "author": "Adie",
      "year": "2005",
      "journal-title": "BMC Bioinformatics"
    },
    {
      "key": "2023012408532753900_b2",
      "doi-asserted-by": "crossref",
      "first-page": "431",
      "DOI": "10.1038/ng0504-431",
      "article-title": "The Genetic Association Database",
      "volume": "36",
      "author": "Becker",
      "year": "2004",
      "journal-title": "Nat. Genet."
    },
    {
      "key": "2023012408532753900_b3",
      "doi-asserted-by": "crossref",
      "first-page": "285",
      "DOI": "10.1093/nar/26.1.285",
      "article-title": "The human gene mutation database",
      "volume": "26",
      "author": "Cooper",
      "year": "1998",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "2023012408532753900_b4",
      "doi-asserted-by": "crossref",
      "first-page": "S110",
      "DOI": "10.1093/bioinformatics/18.suppl_2.S110",
      "article-title": "A similarity-based method for genome-wide prediction of disease-relevant human genes",
      "volume": "18",
      "author": "Freudenberg",
      "year": "2002",
      "journal-title": "Bioinformatics"
    },
    {
      "key": "2023012408532753900_b5",
      "doi-asserted-by": "crossref",
      "first-page": "52",
      "DOI": "10.1093/nar/30.1.52",
      "article-title": "Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders",
      "volume": "30",
      "author": "Hamosh",
      "year": "2002",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "2023012408532753900_b6",
      "doi-asserted-by": "crossref",
      "first-page": "3108",
      "DOI": "10.1093/nar/gkh605",
      "article-title": "Genome-wide identification of genes likely to be involved in human genetic disease",
      "volume": "32",
      "author": "Lopez-Bigas",
      "year": "2004",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "2023012408532753900_b7",
      "doi-asserted-by": "crossref",
      "first-page": "1275",
      "DOI": "10.1093/bioinformatics/btg153",
      "article-title": "Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation",
      "volume": "19",
      "author": "Lord",
      "year": "2003",
      "journal-title": "Bioinformatics"
    },
    {
      "key": "2023012408532753900_b8",
      "doi-asserted-by": "crossref",
      "first-page": "119",
      "DOI": "10.1186/gb-2003-4-10-119",
      "article-title": "New methods for finding disease-susceptibility genes: impact and potential",
      "volume": "4",
      "author": "McCarthy",
      "year": "2003",
      "journal-title": "Genome Biol."
    },
    {
      "key": "2023012408532753900_b9",
      "doi-asserted-by": "crossref",
      "first-page": "316",
      "DOI": "10.1038/ng895",
      "article-title": "Association of genes to genetically inherited diseases using data mining",
      "volume": "31",
      "author": "Perez-Iratxeta",
      "year": "2002",
      "journal-title": "Nat. Genet."
    },
    {
      "key": "2023012408532753900_b10",
      "doi-asserted-by": "crossref",
      "first-page": "4465",
      "DOI": "10.1073/pnas.012025199",
      "article-title": "Large-scale analysis of the human and mouse transcriptomes",
      "volume": "99",
      "author": "Su",
      "year": "2002",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "2023012408532753900_b11",
      "doi-asserted-by": "crossref",
      "first-page": "1544",
      "DOI": "10.1093/nar/gki296",
      "article-title": "Integration of text- and data-mining using ontologies successfully selects disease gene candidates",
      "volume": "33",
      "author": "Tiffin",
      "year": "2005",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "2023012408532753900_b12",
      "doi-asserted-by": "crossref",
      "first-page": "R75",
      "DOI": "10.1186/gb-2003-4-11-r75",
      "article-title": "POCUS: mining genomic sequence annotation to predict disease genes",
      "volume": "4",
      "author": "Turner",
      "year": "2003",
      "journal-title": "Genome Biol."
    },
    {
      "key": "2023012408532753900_b13",
      "doi-asserted-by": "crossref",
      "first-page": "57",
      "DOI": "10.1038/sj.ejhg.5200918",
      "article-title": "A new web-based data mining tool for the identification of candidate genes for human genetic disorders",
      "volume": "11",
      "author": "Van Driel",
      "year": "2003",
      "journal-title": "Eur. J. Hum. Genet."
    }
  ],
  "container-title": "Bioinformatics",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://academic.oup.com/bioinformatics/article-pdf/22/6/773/48839673/bioinformatics_22_6_773.pdf",
      "content-type": "application/pdf",
      "content-version": "vor",
      "intended-application": "syndication"
    },
    {
      "URL": "https://academic.oup.com/bioinformatics/article-pdf/22/6/773/48839673/bioinformatics_22_6_773.pdf",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2023,
        1,
        24
      ]
    ],
    "date-time": "2023-01-24T09:32:16Z",
    "timestamp": 1674552736000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://academic.oup.com/bioinformatics/article/22/6/773/295499"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2006,
        1,
        19
      ]
    ]
  },
  "references-count": 13,
  "journal-issue": {
    "issue": "6",
    "published-print": {
      "date-parts": [
        [
          2006,
          3,
          15
        ]
      ]
    }
  },
  "URL": "http://dx.doi.org/10.1093/bioinformatics/btk031",
  "relation": {},
  "ISSN": [
    "1367-4811",
    "1367-4803"
  ],
  "subject": [],
  "published-other": {
    "date-parts": [
      [
        2006,
        3,
        15
      ]
    ]
  },
  "published": {
    "date-parts": [
      [
        2006,
        1,
        19
      ]
    ]
  }
}