The DOI matches its Crossref record; 28 of the 28 references it cites were found in a registry or an index.
seqMINER: an integrated ChIP-seq data interpretation platform
Open accessAbstract
In a single experiment, chromatin immunoprecipitation combined with high throughput sequencing (ChIP-seq) provides genome-wide information about a given covalent histone modification or transcription factor occupancy. However, time efficient bioinformatics resources for extracting biological meaning out of these gigabyte-scale datasets are often a limiting factor for data interpretation by biologists. We created an integrated portable ChIP-seq data interpretation platform called seqMINER, with optimized performances for efficient handling of multiple genome-wide datasets. seqMINER allows comparison and integration of multiple ChIP-seq datasets and extraction of qualitative as well as quantitative information. seqMINER can handle the biological complexity of most experimental situations and proposes methods to the user for data classification according to the analysed features. In addition, through multiple graphical representations, seqMINER allows visualization and modelling of general as well as specific patterns in a given dataset. To demonstrate the efficiency of seqMINER, we have carried out a comprehensive analysis of genome-wide chromatin modification data in mouse embryonic stem cells to understand the global epigenetic landscape and its change through cellular differentiation.
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Cites
Model-based Analysis of ChIP-Seq (MACS)
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The Human Genome Browser at UCSC
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A bivalent chromatin structure marks key developmental genes in embryonic stem cells
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Genome-Wide Mapping of in Vivo Protein-DNA Interactions
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Histone modifications at human enhancers reflect global cell-type-specific gene expression
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Polycomb complexes repress developmental regulators in murine embryonic stem cells
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Cited by
A Validated Regulatory Network for Th17 Cell Specification
Ciofani, M., Madar, A., Galan, C., Sellars, M., Mace, K., Pauli, F., Agarwal, A., Huang, W., Parkurst, C. N., Muratet, M., et al. (2012) · Cell · doi:10.1016/j.cell.2012.09.016 · Cited by 1,160
The cohesin release factor WAPL restricts chromatin loop extension
Haarhuis, J. H. I., van der Weide, R. H., Blomen, V. A., Yáñez-Cuna, J. O., Amendola, M., van Ruiten, M. S., Krijger, P. H. L., Teunissen, H., Medema, R. H., van Steensel, B., et al. (2017) · Cell · doi:10.1016/j.cell.2017.04.013 · Cited by 793
T-cell factor 4 and β-catenin chromatin occupancies pattern zonal liver metabolism in mice
Gougelet, A., Torre, C., Veber, P., Sartor, C., Bachelot, L., Denechaud, P.-D., Godard, C., Moldes, M., Burnol, A.-F., Dubuquoy, C., et al. (2014) · Hepatology · doi:10.1002/hep.26924 · Cited by 190
Self-citationStaber, P. B., Zhang, P., Ye, M., Welner, R. S., Nombela-Arrieta, C., Bach, C., Kerenyi, M., Bartholdy, B. A., Zhang, H., Alberich-Jordà, M., et al. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.01.007 · Cited by 158
Moutier, E., Ye, T., Choukrallah, M.-A., Urban, S., Osz, J., Chatagnon, A., Delacroix, L., Langer, D., Rochel, N., Moras, D., et al. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.361790 · Cited by 163
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Metadata
- Authors
- Ye, T., Krebs, A. R., Choukrallah, M.-A., Keime, C., Plewniak, F., Davidson, I., & Tora, L.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-12-21
- Volume
- 39
- Issue
- 6
- Pages
- e35-e35
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2086376086
- Cited by
- 417
- References
- 28
- FWCI
- 7.80
- Type
- journal article
- Language
- en
- Open access
- gold
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- Ye, T., Krebs, A. R., Choukrallah, M.-A., Keime, C., Plewniak, F., Davidson, I., & Tora, L. (2011). seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Research. https://doi.org/10.1093/nar/gkq1287
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