DOI: 10.1073/pnas.0601180103. Model-based analysis of tiling-arrays for ChIP-chip

Model-based analysis of tiling-arrays for ChIP-chip

10.1073/pnas.0601180103

Crossref journal-article

Proceedings of the National Academy of Sciences

Proceedings of the National Academy of Sciences (341)

Abstract

We propose a fast and powerful analysis algorithm, titled Model-based Analysis of Tiling-arrays (MAT), to reliably detect regions enriched by transcription factor chromatin immunoprecipitation (ChIP) on Affymetrix tiling arrays (ChIP-chip). MAT models the baseline probe behavior by considering probe sequence and copy number on each array. It standardizes the probe value through the probe model, eliminating the need for sample normalization. MAT uses an innovative function to score regions for ChIP enrichment, which allows robust P value and false discovery rate calculations. MAT can detect ChIP regions from a single ChIP sample, multiple ChIP samples, or multiple ChIP samples with controls with increasing accuracy. The single-array ChIP region detection feature minimizes the time and monetary costs for laboratories newly adopting ChIP-chip to test their protocols and antibodies and allows established ChIP-chip laboratories to identify samples with questionable quality that might contaminate their data. MAT is developed in open-source Python and is available at http://chip.dfci.harvard.edu/∼wli/MAT . The general framework presented here can be extended to other oligonucleotide microarrays and tiling array platforms.

Bibliography

Johnson, W. E., Li, W., Meyer, C. A., Gottardo, R., Carroll, J. S., Brown, M., & Liu, X. S. (2006). Model-based analysis of tiling-arrays for ChIP-chip. Proceedings of the National Academy of Sciences, 103(33), 12457â12462.

Authors 7

W. Evan Johnson (first)
Wei Li (additional)
Clifford A. Meyer (additional)
Raphael Gottardo (additional)
Jason S. Carroll (additional)
Myles Brown (additional)
X. Shirley Liu (additional)

References 14 Referenced 340

10.1038/35054095
10.1038/ng569
10.1126/science.290.5500.2306
10.1038/nature02800
10.1016/S0092-8674(04)00127-8
10.1093/bioinformatics/bti1046
S. Keles, M. van de Laan, S. Dudoit, S. E. Cawley Multiple Testing Methods For ChIP-Chip High Density Oligonucleotide Array Data (Univ. of California, Berkeley, University of California Berkeley Division of Biostatistics Working Paper Series No. 147. (2004). / Multiple Testing Methods For ChIP-Chip High Density Oligonucleotide Array Data by Keles S. (2004)
10.1093/bioinformatics/bti593
10.1016/j.cell.2005.05.008
10.1093/bioinformatics/19.2.185
10.1093/nar/gkg283
Z. Wu, R. A. Irizarry, R. Gentleman, F. M. Murillo, F. Spencer A Model Based Background Adjustment for Oligonucleotide Expression Arrays: Technical Report (Department of Biostatistics, Johns Hopkins Univ., Baltimore, Johns Hopkins University Department of Biostatistics Working Paper No. 1. (2003). / A Model Based Background Adjustment for Oligonucleotide Expression Arrays: Technical Report by Wu Z. (2003)
10.1093/nar/27.2.573
10.1101/gr.187101

Dates

Type	When
Created	19 years ago (Aug. 8, 2006, 11:38 p.m.)
Deposited	3 years, 4 months ago (April 12, 2022, 3:40 p.m.)
Indexed	11 months, 2 weeks ago (Sept. 15, 2024, 7:11 a.m.)
Issued	19 years ago (Aug. 15, 2006)
Published	19 years ago (Aug. 15, 2006)
Published Online	19 years ago (Aug. 15, 2006)
Published Print	19 years ago (Aug. 15, 2006)

Funders 0

None

BibTeX

@article{Johnson_2006, title={Model-based analysis of tiling-arrays for ChIP-chip}, volume={103}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.0601180103}, DOI={10.1073/pnas.0601180103}, number={33}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Johnson, W. Evan and Li, Wei and Meyer, Clifford A. and Gottardo, Raphael and Carroll, Jason S. and Brown, Myles and Liu, X. Shirley}, year={2006}, month=aug, pages={12457–12462} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2024,
        9,
        15
      ]
    ],
    "date-time": "2024-09-15T11:11:48Z",
    "timestamp": 1726398708165
  },
  "reference-count": 14,
  "publisher": "Proceedings of the National Academy of Sciences",
  "issue": "33",
  "content-domain": {
    "domain": [
      "www.pnas.org"
    ],
    "crossmark-restriction": true
  },
  "published-print": {
    "date-parts": [
      [
        2006,
        8,
        15
      ]
    ]
  },
  "abstract": "<jats:p>\n            We propose a fast and powerful analysis algorithm, titled Model-based Analysis of Tiling-arrays (MAT), to reliably detect regions enriched by transcription factor chromatin immunoprecipitation (ChIP) on Affymetrix tiling arrays (ChIP-chip). MAT models the baseline probe behavior by considering probe sequence and copy number on each array. It standardizes the probe value through the probe model, eliminating the need for sample normalization. MAT uses an innovative function to score regions for ChIP enrichment, which allows robust\n            <jats:italic>P</jats:italic>\n            value and false discovery rate calculations. MAT can detect ChIP regions from a single ChIP sample, multiple ChIP samples, or multiple ChIP samples with controls with increasing accuracy. The single-array ChIP region detection feature minimizes the time and monetary costs for laboratories newly adopting ChIP-chip to test their protocols and antibodies and allows established ChIP-chip laboratories to identify samples with questionable quality that might contaminate their data. MAT is developed in open-source Python and is available at\n            <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" ext-link-type=\"uri\" xlink:href=\"http://chip.dfci.harvard.edu/~wli/MAT\">http://chip.dfci.harvard.edu/\u223cwli/MAT</jats:ext-link>\n            . The general framework presented here can be extended to other oligonucleotide microarrays and tiling array platforms.\n          </jats:p>",
  "DOI": "10.1073/pnas.0601180103",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2006,
        8,
        9
      ]
    ],
    "date-time": "2006-08-09T03:38:47Z",
    "timestamp": 1155094727000
  },
  "page": "12457-12462",
  "update-policy": "http://dx.doi.org/10.1073/pnas.cm10313",
  "source": "Crossref",
  "is-referenced-by-count": 340,
  "title": "Model-based analysis of tiling-arrays for ChIP-chip",
  "prefix": "10.1073",
  "volume": "103",
  "author": [
    {
      "given": "W. Evan",
      "family": "Johnson",
      "sequence": "first",
      "affiliation": [
        {
          "name": "*Department of Biostatistics and Computational Biology, Dana\u2013Farber Cancer Institute, 44 Binney Street, Boston, MA 02115;"
        },
        {
          "name": "Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115; and"
        }
      ]
    },
    {
      "given": "Wei",
      "family": "Li",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "*Department of Biostatistics and Computational Biology, Dana\u2013Farber Cancer Institute, 44 Binney Street, Boston, MA 02115;"
        },
        {
          "name": "Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115; and"
        }
      ]
    },
    {
      "given": "Clifford A.",
      "family": "Meyer",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "*Department of Biostatistics and Computational Biology, Dana\u2013Farber Cancer Institute, 44 Binney Street, Boston, MA 02115;"
        },
        {
          "name": "Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115; and"
        }
      ]
    },
    {
      "given": "Raphael",
      "family": "Gottardo",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Department of Statistics, University of British Columbia, 333-6356 Agricultural Road, Vancouver, BC, Canada V6T 1Z2"
        }
      ]
    },
    {
      "given": "Jason S.",
      "family": "Carroll",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Department of Medical Oncology, Dana\u2013Faber Cancer Institute and Harvard Medical School, 44 Binney Street, Boston, MA 02115;"
        }
      ]
    },
    {
      "given": "Myles",
      "family": "Brown",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Department of Medical Oncology, Dana\u2013Faber Cancer Institute and Harvard Medical School, 44 Binney Street, Boston, MA 02115;"
        }
      ]
    },
    {
      "given": "X. Shirley",
      "family": "Liu",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "*Department of Biostatistics and Computational Biology, Dana\u2013Farber Cancer Institute, 44 Binney Street, Boston, MA 02115;"
        },
        {
          "name": "Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115; and"
        }
      ]
    }
  ],
  "member": "341",
  "published-online": {
    "date-parts": [
      [
        2006,
        8,
        15
      ]
    ]
  },
  "reference": [
    {
      "key": "e_1_3_4_1_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/35054095"
    },
    {
      "key": "e_1_3_4_2_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/ng569"
    },
    {
      "key": "e_1_3_4_3_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.290.5500.2306"
    },
    {
      "key": "e_1_3_4_4_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nature02800"
    },
    {
      "key": "e_1_3_4_5_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0092-8674(04)00127-8"
    },
    {
      "key": "e_1_3_4_6_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/bioinformatics/bti1046"
    },
    {
      "key": "e_1_3_4_7_2",
      "volume-title": "Multiple Testing Methods For ChIP-Chip High Density Oligonucleotide Array Data",
      "author": "Keles S.",
      "year": "2004",
      "unstructured": "S. Keles, M. van de Laan, S. Dudoit, S. E. Cawley Multiple Testing Methods For ChIP-Chip High Density Oligonucleotide Array Data (Univ. of California, Berkeley, University of California Berkeley Division of Biostatistics Working Paper Series No. 147. (2004)."
    },
    {
      "key": "e_1_3_4_8_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/bioinformatics/bti593"
    },
    {
      "key": "e_1_3_4_9_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/j.cell.2005.05.008"
    },
    {
      "key": "e_1_3_4_10_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/bioinformatics/19.2.185"
    },
    {
      "key": "e_1_3_4_11_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/nar/gkg283"
    },
    {
      "key": "e_1_3_4_12_2",
      "volume-title": "A Model Based Background Adjustment for Oligonucleotide Expression Arrays: Technical Report",
      "author": "Wu Z.",
      "year": "2003",
      "unstructured": "Z. Wu, R. A. Irizarry, R. Gentleman, F. M. Murillo, F. Spencer A Model Based Background Adjustment for Oligonucleotide Expression Arrays: Technical Report (Department of Biostatistics, Johns Hopkins Univ., Baltimore, Johns Hopkins University Department of Biostatistics Working Paper No. 1. (2003)."
    },
    {
      "key": "e_1_3_4_13_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/nar/27.2.573"
    },
    {
      "key": "e_1_3_4_14_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1101/gr.187101"
    }
  ],
  "container-title": "Proceedings of the National Academy of Sciences",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://pnas.org/doi/pdf/10.1073/pnas.0601180103",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2022,
        4,
        12
      ]
    ],
    "date-time": "2022-04-12T19:40:16Z",
    "timestamp": 1649792416000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://pnas.org/doi/full/10.1073/pnas.0601180103"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2006,
        8,
        15
      ]
    ]
  },
  "references-count": 14,
  "journal-issue": {
    "issue": "33",
    "published-print": {
      "date-parts": [
        [
          2006,
          8,
          15
        ]
      ]
    }
  },
  "alternative-id": [
    "10.1073/pnas.0601180103"
  ],
  "URL": "http://dx.doi.org/10.1073/pnas.0601180103",
  "relation": {},
  "ISSN": [
    "0027-8424",
    "1091-6490"
  ],
  "subject": [],
  "container-title-short": "Proc. Natl. Acad. Sci. U.S.A.",
  "published": {
    "date-parts": [
      [
        2006,
        8,
        15
      ]
    ]
  },
  "assertion": [
    {
      "value": "2006-02-13",
      "order": 0,
      "name": "received",
      "label": "Received",
      "group": {
        "name": "publication_history",
        "label": "Publication History"
      }
    },
    {
      "value": "2006-08-15",
      "order": 2,
      "name": "published",
      "label": "Published",
      "group": {
        "name": "publication_history",
        "label": "Publication History"
      }
    }
  ]
}