The DOI matches its Crossref record; 21 of the 21 references it cites were found in a registry or an index.
Genome-wide identification of peroxisome proliferator response elements using integrated computational genomics
Open accessAbstract
Peroxisome proliferator-activated receptor (PPAR) agonists are currently used therapeutically in humans, even though many of their direct gene targets are unknown. Because PPARs can directly regulate gene expression through peroxisome proliferator response elements (PPREs), we pursued the computational prediction of PPREs on a genome-wide scale. Contrary to current hypotheses, PPREs are not isotype-specific, nor do flanking nucleotides confer additional information. However, a position weight matrix-based search for PPREs within upstream conserved elements yielded sufficient selectivity for a genome-wide search. Additionally, a novel motif occurring with greater prevalence than PPREs was revealed. Microarray and gene ontology analyses further validated our search technique and provided new functional clusters of genes that were not previously known to be directly regulated by PPARs (e.g., chromatin remodeling, DNA damage response, Wnt, and mitogen-activated protein kinase signaling). This first genome-wide library of high-confidence predicted PPAR target genes will be a valuable resource to PPAR biologists.
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“The PPAR-RXR dimer binds peroxisome proliferator response elements (PPRE) to activate the transcription of genes within the ATP-binding cassette (ABC) family and genes involved in FA scavenging and lipid metabolism [50,51,76,79].”
From Lipoprotein Lipase Regulates Microglial Lipid Droplet Accumulation (2021) · cites this paper as [50]
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“PPAR agonists have been shown to protect against neuronal death and neuroinflammation, and also to promote CNS repair [50,51].”
From Lipoprotein Lipase Regulates Microglial Lipid Droplet Accumulation (2021) · cites this paper as [50]
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Cites
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
WebLogo: A Sequence Logo Generator: Figure 1Preprint
Crooks, G. E., Hon, G. C., Chandonia, J., & Brenner, S. E. (2004) · Genome Research · doi:10.1101/gr.849004 · Cited by 12,480
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
Fitting a mixture model by expectation maximization to discover motifs in biopolymers.
Bailey, T. L., & Elkan, C. (1994) · PubMed · Cited by 4,982
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 3,971 · cited 1×
“These elements, provided via the human Most Conserved track at UCSC, are conserved in space (neighboring nucleotides) and time (human, chimp, mouse, rat, dog, chicken, fugu, and zebrafish genomes), as identified by the phylogenetic hidden Markov model of Siepel et al. ( 16 ).”
BackgroundThe UCSC Table Browser data retrieval tool
Karolchik, D. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh103 · Cited by 2,314
Genome sequence of the Brown Norway rat yields insights into mammalian evolution
Gibbs, R. A., Weinstock, G. M., Metzker, M. L., Muzny, D. M., Sodergren, E. J., Scherer, S. E., Scott, G., Steffen, D. L., Worley, K. C., Burch, P. E., et al. (2004) · Nature · doi:10.1038/nature02426 · Cited by 2,170
Hertz, G. Z., & Stormo, G. D. (1999) · Bioinformatics · doi:10.1093/bioinformatics/15.7.563 · Cited by 1,246
MATCHTM: a tool for searching transcription factor binding sites in DNA sequences
Kel, A. E. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg585 · Cited by 1,095
TRANSFAC: a database on transcription factors and their DNA binding sites
Wingender, E. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.1.238 · Cited by 1,064
Doniger, S. W., Salomonis, N., Dahlquist, K. D., VRANIZAN, K. M., Lawlor, S. C., & Conklin, B. R. (2003) · Genome biology · doi:10.1186/gb-2003-4-1-r7 · Cited by 865
Juge-Aubry, C. E., Pernin, A., Favez, T., Burger, A., Wahli, W., Meier, C. A., & Desvergne, B. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.40.25252 · Cited by 385
IJpenberg, A., Jeannin, E., Wahli, W., & Desvergne, B. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.32.20108 · Cited by 363
Modeling within-motif dependence for transcription factor binding site predictions
Zhou, Q., & Liu, J. S. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth006 · Cited by 151
Yamazaki, K., Kuromitsu, J., & Tanaka, I. (2002) · Biochemical and Biophysical Research Communications · doi:10.1006/bbrc.2001.6319 · Cited by 108
Hsiao, A., Worrall, D. S., Olefsky, J. M., & Subramaniam, S. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth371 · Cited by 89
Gene expression profiling of potential PPARγ target genes in mouse aorta
Keen, H. L., Ryan, M. J., Beyer, A., Mathur, S. N., Scheetz, T. E., Gackle, B. D., Faraci, F. M., Casavant, T. L., & Sigmund, C. D. (2004) · Physiological Genomics · doi:10.1152/physiolgenomics.00027.2004 · Cited by 49
Yadetie, F., Lægreid, A., Bakke, I., Kusnierczyk, W., Komorowski, J., Waldum, H. L., & Sandvik, A. K. (2003) · Physiological Genomics · doi:10.1152/physiolgenomics.00064.2003 · Cited by 39
Parton, L. E., Diraison, F., Neill, S. E., Ghosh, S., Rubino, M. A., Bisi, J., Briscoe, C. P., & Rutter, G. A. (2004) · American Journal of Physiology-Endocrinology and Metabolism · doi:10.1152/ajpendo.00016.2004 · Cited by 34
Yu, S., Viswakarma, N., Batra, S. K., Rao, M. S., & Reddy, J. K. (2004) · Biochimie · doi:10.1016/j.biochi.2004.09.015 · Cited by 32
Kassam, A., Hunter, J., Rachubinski, R. A., & Capone, J. P. (1998) · Molecular and Cellular Endocrinology · doi:10.1016/s0303-7207(98)00085-9 · Cited by 21
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Merner, N. D., Hodgkinson, K. A., Haywood, A. F. M., Connors, S. P., French, V. M., Drenckhahn, J., Kupprion, C., Ramadanova, K., Thierfelder, L., McKenna, W. J., et al. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2008.01.010 · Cited by 528
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Martin, M. T., Dix, D. J., Judson, R., Kavlock, R. J., Reif, D. M., Richard, A. M., Rotroff, D. M., Romanov, S., Medvedev, A. V., Poltoratskaya, N., et al. (2010) · Chemical Research in Toxicology · doi:10.1021/tx900325g · Cited by 217
Metadata
- Authors
- Lemay, D. G., & Hwang, D. H.
- Affiliations
- Agricultural Research Service (US)
- Venue
- Journal of Lipid Research
- Publisher
- Elsevier BV
- Published
- 2006-07
- Volume
- 47
- Issue
- 7
- Pages
- 1583-1587
- ISSN
- 0022-2275 (ISSN-L)
- OpenAlex
- W2147427406
- Cited by
- 143
- References
- 21
- Citations by year
- 2026: 1 · 2025: 3 · 2023: 2 · 2022: 3 · 2021: 6 · 2020: 3 · 2019: 5 · 2018: 12 · 2017: 4 · 2016: 4 · 2015: 6 · 2014: 8 · 2013: 11 · 2012: 14
- FWCI
- 5.31
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Lipid Research (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- U.S. Department of Agriculture (01A095Rev)
- National Institutes of Health
- Agricultural Research Service
- National Institute of Diabetes and Digestive and Kidney Diseases (DK-064007, R01DK064007)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Peroxisome Proliferator-Activated Receptors
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Nutrition, Genetics, and Disease
- Keywords
- peroxisome proliferator response element, peroxisome proliferator-activated receptors, PPAR target genes, transcription factor binding site prediction, position weight matrices, PPAR agonists, chromatin remodeling, DNA damage response, Wnt signaling, MAPK signaling
- MeSH terms
- Animals, DNA, Gene Expression Regulation, Humans, Gene Library, Genome, Human, Conserved Sequence, Computational Biology, Oligonucleotide Array Sequence Analysis, Genomics, Peroxisome Proliferator-Activated Receptors, Mice, Rats
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