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Cited by 56Genetic Syndromes and ImprintingGenomics and Chromatin DynamicsChromosomal and Genetic Variations

WAMIDEX: A web atlas of murine genomic imprinting and differential expression

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Schulz, Reiner, Woodfine, Kathryn, Menheniott, Trevelyan R., Bourc'his, Deborah, Bestor, Timothy, Oakey, Rebecca J.·2008·Epigenetics
DOI 10.4161/epi.3.2.5900PMC PMC2492384
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Abstract

The mouse is an established model organism for the study of genomic imprinting. Mice with genetic material originating from only one parent (e.g., mice with uniparental chromosomal duplications) or gene mutations leading to epigenetic deficiencies have proven to be particularly useful tools. In the process of our studies we have accumulated a large set of expression microarray measurements in samples derived from these types of mice. Here, we present the collation of these and third-party microarray data that are relevant to genomic imprinting into a Web Atlas of Murine genomic Imprinting and Differential EXpression (WAMIDEX: https://atlas.genetics.kcl.ac.uk). WAMIDEX integrates the most comprehensive literature-derived catalog of murine imprinted genes to date with a genome browser that makes the microarray data immediately accessible in annotation-rich genomic context. In addition, WAMIDEX exemplifies the use of the self-organizing map method for the discovery of novel imprinted genes from microarray data. The parent-of-origin-specific expression of imprinted genes is frequently limited to specific tissues or developmental stages, a fact that the atlas reflects in its design and data content.

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  • Where array features overlap iDMRs, monoallelic methylation at approximately 50% (β=0.5) is expected.

    “where array features overlap these, we would expect monoallelic (therefore 50% (β=0.5)) methylation.”

    From A data-driven approach to preprocessing Illumina 450K methylation array data (2013) · cites this paper as [15]

    The Introduction describes methylation differences between maternal and paternal alleles at imprinting control regions, and the Methods say most such regions are methylated on the maternal allele. That supports the monoallelic premise, but the paper does not give an expected 50% methylation value or β=0.5 reading for array features overlapping iDMRs; its described microarrays measure gene expression. (LLM, conf=0.82)

    Experimental — accuracy not yet measured

  • Stable iDMRs have been characterized for 25 human imprinting regions.

    “Stable iDMRs have been characterized for 25 human imprinting regions [15,16]”

    From A data-driven approach to preprocessing Illumina 450K methylation array data (2013) · cites this paper as [15]

    The Introduction describes imprinting control regions and reports approximately 50 human imprinted genes, but it does not give a count of human regions with stable iDMRs. Searches for “25 human imprinting regions” and “human differentially methylated regions” found no passage in our copy supporting the claimed 25 regions. (LLM, conf=0.72)

    Experimental — accuracy not yet measured

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Cited by

Sorted by citations

Authors
Schulz, R., Woodfine, K., Menheniott, T. R., Bourc'his, D., Bestor, T., & Oakey, R. J.
Affiliations
  • St Thomas' Hospital (GB)
  • Inserm (FR)
ORCID
Venue
Epigenetics
Publisher
Informa UK Limited
Published
2008-03-24
Volume
3
Issue
2
Pages
89-96
ISSN
  • 1559-2294 (ISSN-L)
  • 1559-2308
DOI
10.4161/epi.3.2.5900
PMC
PMC2492384
OpenAlex
W2042674727
Cited by
56
References
1
Citations by year
2024: 1 · 2023: 1 · 2022: 2 · 2021: 2 · 2020: 2 · 2019: 2 · 2018: 3 · 2017: 2 · 2016: 4 · 2015: 6 · 2014: 6 · 2013: 7 · 2012: 4
FWCI
2.67
Type
journal article
Language
en
Open access
Licence
cc-by-nc
Locations
  • Epigenetics (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • Research Portal (King's College London) (submittedVersion)
Funders
  • Wellcome Trust (071002)
  • Directorate for Biological Sciences
  • Medical Research Council
  • Biotechnology and Biological Sciences Research Council
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Syndromes and Imprinting
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
Keywords
genomic imprinting, imprinted genes, mice, differential gene expression, parent-of-origin expression, epigenetic mutations, self-organizing maps, genome browser, web atlas
MeSH terms
Animals, Genome, Genomic Imprinting, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Databases, Nucleic Acid, Mice

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