The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
Open accessAbstract
We report a novel resource (m ethylation p rofiles o f D NA, or mPod) for human genome-wide tissue-specific DNA methylation profiles. mPod consists of three fully integrated parts, genome-wide DNA methylation reference profiles of 13 normal somatic tissues, placenta, sperm, and an immortalized cell line, a visualization tool that has been integrated with the Ensembl genome browser and a new algorithm for the analysis of immunoprecipitation-based DNA methylation profiles. We demonstrate the utility of our resource by identifying the first comprehensive genome-wide set of tissue-specific differentially methylated regions (tDMRs) that may play a role in cellular identity and the regulation of tissue-specific genome function. We also discuss the implications of our findings with respect to the regulatory potential of regions with varied CpG density, gene expression, transcription factor motifs, gene ontology, and correlation with other epigenetic marks such as histone modifications.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Takahashi, K., & Yamanaka, S. (2006) · Cell · doi:10.1016/j.cell.2006.07.024 · Cited by 26,673
DNA methylation patterns and epigenetic memory
Bird, A. (2002) · Genes & Development · doi:10.1101/gad.947102 · Cited by 7,124
High-Resolution Profiling of Histone Methylations in the Human Genome
Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., & Zhao, K. (2007) · Cell · doi:10.1016/j.cell.2007.05.009 · Cited by 6,845
The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223
A gene atlas of the mouse and human protein-encoding transcriptomes
Su, A. I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K. A., Block, D., Zhang, J., Soden, R., Hayakawa, M., Kreiman, G., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0400782101 · Cited by 3,475
Boyes, J., & Bird, A. (1992) · The EMBO Journal · doi:10.1002/j.1460-2075.1992.tb05055.x · Cited by 471
Cited by
High density DNA methylation array with single CpG site resolution
Bibikova, M., Barnes, B., Tsan, C., Ho, V., Klotzle, B., Le, J. M., Delano, D., Zhang, L., Schroth, G. P., Gunderson, K. L., et al. (2011) · Genomics · doi:10.1016/j.ygeno.2011.07.007 · Cited by 1,727
SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips
Maksimovic, J., Gordon, L., & Oshlack, A. (2012) · Genome Biology · doi:10.1186/gb-2012-13-6-r44 · Cited by 826
Dayeh, T., Volkov, P., Salö, S., Hall, E., Nilsson, E., Olsson, A. H., Kirkpatrick, C. L., Wollheim, C. B., Eliasson, L., Rönn, T., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004160 · Cited by 523
DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns
Lokk, K., Modhukur, V., Rajashekar, B., Märtens, K., Mägi, R., Kolde, R., Koltšina, M., Nilsson, T. K., Vilo, J., Salumets, A., et al. (2014) · Genome Biology · doi:10.1186/gb-2014-15-4-r54 · Cited by 444
Volkmar, M., Dedeurwaerder, S., Cunha, D. A., Ndlovu, M. N., Defrance, M., Deplus, R., Calonne, E., Volkmar, U., Igoillo‐Esteve, M., Naamane, N., et al. (2012) · The EMBO Journal · doi:10.1038/emboj.2011.503 · Cited by 420
“Supplementary Table S4). differential DNA methylation and gene expression (Illingworth et al , 2008) or found a small but significant set of genes with anticorrelation between changes in promoter methylation and gene expression (Rakyan et al , 2008).”
Metadata
- Authors
- Rakyan, V. K., Down, T. A., Thorne, N. P., Flicek, P., Kulesha, E., Gräf, S., Tomazou, E. M., Bäckdahl, L., Johnson, N., Herberth, M., Howe, K. L., Jackson, D. K., Miretti, M. M., Fiegler, H., Marioni, J. C., Birney, E., Hubbard, T. J. P., Carter, N. P., Tavaré, S., & Beck, S.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2008-06-24
- Volume
- 18
- Issue
- 9
- Pages
- 1518-1529
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2101214870
- Cited by
- 378
- References
- 6
- Type
- posted content
- Language
- en
- Open access
- hybrid
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). https://app.cochat.ai/papers/10.1101/gr.077479.108
- The paper
- Rakyan, V. K., Down, T. A., Thorne, N. P., Flicek, P., Kulesha, E., Gräf, S., Tomazou, E. M., Bäckdahl, L., Johnson, N., Herberth, M., Howe, K. L., Jackson, D. K., Miretti, M. M., Fiegler, H., Marioni, J. C., Birney, E., Hubbard, T. J. P., Carter, N. P., Tavaré, S., & Beck, S. (2008). An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Research. https://doi.org/10.1101/gr.077479.108
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
