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.
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.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“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]
Experimental — accuracy not yet measured
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
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
Cited by
Sorted by citations
Items 101–144 of 144
Distance-Based Phylogenetic Methods
Xia, X. (2018) · Springer eBooks · doi:10.1007/978-3-319-90684-3_15 · Cited by 7
Haustrate, A., Hantute-Ghesquier, A., Prevarskaya, N. B., & Lehen’kyi, V. (2019) · Cell Calcium · doi:10.1016/j.ceca.2019.04.006 · Cited by 6
RetractedNucleotide Substitution Models and Evolutionary Distances
Xia, X. (2018) · Springer eBooks · doi:10.1007/978-3-319-90684-3_12 · Cited by 5
Identifying kinase targets of PPARγ in human breast cancer
Kandel, A., Dhillon, S. K., Prabaharan, C. B., Hisham, S. F. B., Rajamanickam, K., Napper, S., Chidambaram, S. B., Essa, M. M., Yang, J., & Sakharkar, M. K. (2021) · Journal of drug targeting · doi:10.1080/1061186x.2021.1877719 · Cited by 4
Orgil, B., Spaulding, M. S., Smith, H. P., Baba, Z., Alberson, N. R., Batsaikhan, E., Towbin, J. A., & Purevjav, E. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26146856 · Cited by 4
Position Weight Matrix and Perceptron
Xia, X. (2018) · Springer eBooks · doi:10.1007/978-3-032-18842-7_3 · Cited by 3
Bioinformatics and Translation Initiation
Xia, X. (2018) · Springer eBooks · doi:10.1007/978-3-032-18842-7_10 · Cited by 3
Alternatively Spliced Landscape of PPARγ mRNA in Podocytes Is Distinct from Adipose Tissue
Bryant, C., Webb, A., Banks, A. S., Chandler, D. S., Govindarajan, R., & Agrawal, S. (2022) · Cells · doi:10.3390/cells11213455 · Cited by 3
Felicidade, I., Marcarini, J. C., Carreira, C. M., Amarante, M. K., Afman, L. A., Mantovani, M. S., & Ribeiro, L. R. (2014) · Annals of Nutrition and Metabolism · doi:10.1159/000367668 · Cited by 3
Protein Isoelectric Point and Helicobacter pylori
Xia, X. (2018) · Springer eBooks · doi:10.1007/978-3-032-18842-7_14 · Cited by 3
Levitsky, V. G., Ignatieva, E. V., Аман, Е. Э., Merkulova, T. I., Kolchanov, N. A., & Hodgman, C. T. (2008) · Intelligent Data Analysis · doi:10.3233/ida-2008-12506 · Cited by 2
Hurst, T. P. (2013) · ISRN Virology · doi:10.5402/2013/609348 · Cited by 2
Target Gene Identification via Nuclear Receptor Binding Site Prediction
Varga, G. (2010) · Methods in molecular biology · doi:10.1007/978-1-60761-854-6_15 · Cited by 2
Kotlinowski, J., Grochot‐Przeczek, A., Taha, H., Kozakowska, M., Pilecki, B., Skrzypek, K., Bartelik, A., Derlacz, R., Horrevoets, A. J. G., Pap, A., et al. (2014) · Cardiovascular Diabetology · doi:10.1186/preaccept-1453357592137930 · Cited by 2
Hepatic Gene Expression Profiling to Predict Future Lactation Performance in Dairy Cattle
Doelman, J. (2011) · The Atrium (University of Guelph) · Cited by 2
Vohl, M., Badr, M. Z., & Wieczorek, S. (2009) · PPAR Research · doi:10.1155/2009/189091 · Cited by 1
Richardson, K., Schnitzler, G. R., Lai, C., & Ordovás, J. M. (2015) · Circulation Cardiovascular Genetics · doi:10.1161/circgenetics.115.001174 · Cited by 1
Xia, X. (2018) · Springer eBooks · doi:10.1007/978-3-319-90684-3_19 · Cited by 1
The Impact of Whole GenomeIn SilicoScreening for Nuclear Receptor‐Binding Sites in Systems Biology
Carlberg, C., & Heinäniemi, M. (2010) · Wiley eBooks · doi:10.1002/9780470556757.ch13 · Cited by 1
Identification of novel PGRP3 protein -protein interactions using yeast two hybrid systemPreprint
Lin, L.-J., Lee, C. C., Ranganathan, S., Kreth, J., Merritt, J. L., & Prakasam, S. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.12.16.520769 · Cited by 1
Astapova, O., & Leff, T. (2010) · Wiley eBooks · doi:10.1002/9783527629527.ch23
Sequence analysis of chromatin immunoprecipitation data for factors
MacIsaac, K. D., & Fraenkel, E. (2010) · DSpace@MIT (Massachusetts Institute of Technology)
French, V. M. (2008) · Memorial University Research Repository (Memorial University)
Characterization and Promoter Activity Analysis of a New Porcine Gene: NICE-3
Zhang, Z., Mo, D., Ling, F., Wang, C., Li, A., Zhao, X. L., Li, Y., & Chen, Y. (2009) · DNA and Cell Biology · doi:10.1089/dna.2009.0946
The rosiglitazone riddle: DREAMs and nightmares
Misra, A., & Khurana, L. (2007) · Diabetes & Metabolic Syndrome Clinical Research & Reviews · doi:10.1016/j.dsx.2007.06.001
[Drug therapy of type 2 diabetes and cardiovascular prevention: potentials for liraglutide].
Reboldi, G. (2009) · PubMed
PPAR-γ: A Master Metabolic Nuclear Receptor
Onteru, S. K., & Singh, D. (2013) · Journal of Endocrinology & Reproduction · doi:10.18519/jer/2013/v17/75785
PPAR-Alpha Cloning, Expression, and Characterization
Ngo, S. N. T., & McKinnon, R. A. (2012) · Methods in molecular biology · doi:10.1007/978-1-62703-155-4_2
Heat stress-induced PPAR-? enhances HUVEC resistance to oxidant injury
Zhou, B. (2013) · Asian Biomedicine · doi:10.5372/abm.v7i2.21364
ReviewArticle PPAR Ligands as Potential Modifiers of Breast Carcinoma Outcomes
Baranova, A. V. (2008)
Hu, G., Wang, S., & Li, H. (2011) · Journal of Northeast Agricultural University (English edition) · doi:10.1016/s1006-8104(13)60082-3
Shashni, B. (2015) · Terrestrial Environment Research Center (University of Tsukuba)
Richert, S. (2016) · eDiss (Georg-August-Universität Göttingen) · doi:10.53846/goediss-5949
MacLaughlin, S. (2018) · Memorial University Research Repository (Memorial University)
Cabrera, G. B., & Morales, B. P. V. (2015) · Entretextos (en línea, León, Gto.)/Entretextos · doi:10.59057/iberoleon.20075316.201521411
Russo, G. H., Tinoco, G. L. B., Vicari, M. R., Nogueira, R. S., Melo, P. L. G., Torrecilhas, J. A., Curi, R. A., Moriel, P., Baldassini, W. A., Chardulo, L. A. L., et al. (2025) · Frontiers in Animal Science · doi:10.3389/fanim.2025.1533043
Sun, L., Wabitsch, M., Yang, J. P., & Sakharkar, M. K. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.08.687092
Carlberg, C. (2010) · Springer eBooks · doi:10.1007/978-90-481-3303-1_17
Torrecilhas, J. A., Russo, G. H., Tinoco, G. L. B., Melo, P. L. G., Moriel, P., Osório, H., Ribeiro, D. M., Baldassini, W. A., Curi, R. A., Almeida, A. G., et al. (2026) · ACS Agricultural Science & Technology · doi:10.1021/acsagscitech.6c00225
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
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
