The DOI matches its Crossref record; 52 of the 52 references it cites were found in a registry or an index.
Integrating Genetic and Network Analysis to Characterize Genes Related to Mouse Weight
Open accessAbstract
Systems biology approaches that are based on the genetics of gene expression have been fruitful in identifying genetic regulatory loci related to complex traits. We use microarray and genetic marker data from an F2 mouse intercross to examine the large-scale organization of the gene co-expression network in liver, and annotate several gene modules in terms of 22 physiological traits. We identify chromosomal loci (referred to as module quantitative trait loci, mQTL) that perturb the modules and describe a novel approach that integrates network properties with genetic marker information to model gene/trait relationships. Specifically, using the mQTL and the intramodular connectivity of a body weight-related module, we describe which factors determine the relationship between gene expression profiles and weight. Our approach results in the identification of genetic targets that influence gene modules (pathways) that are related to the clinical phenotypes of interest.
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?
In the citing paper
“Subsequently, networks were modeled based on co-expression across a series of perturbations with the genes encoding the transcripts corresponding to the nodes and the correlations to the edges [67–69].”
From Multi-omics approaches to disease (2017) · cites this paper as [67]
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
Emergence of Scaling in Random Networks
Barabási, A.-L., & Albert, R. (1999) · Science · doi:10.1126/science.286.5439.509 · Cited by 36,135
DAVID: Database for Annotation, Visualization, and Integrated Discovery
Dennis, G., Sherman, B. T., Hosack, D. A., Yang, J., Gao, W., Lane, H. C., & Lempicki, R. A. (2003) · Genome Biology · doi:10.1186/gb-2003-4-5-p3 · Cited by 9,327
Network biology: understanding the cell's functional organization
Barabási, A.-L., & Oltvai, Z. N. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1272 · Cited by 7,903
Error and attack tolerance of complex networks
Albert, R., Jeong, H., & Barabási, A.-L. (2000) · Nature · doi:10.1038/35019019 · Cited by 7,534
Error and attack tolerance of complex networksPreprint
Albert, R., Jeong, H., & Barabási, A.-Ĺ. (2000) · Cited by 6,554
A General Framework for Weighted Gene Co-Expression Network Analysis
Zhang, B., & Horvath, S. (2005) · Statistical Applications in Genetics and Molecular Biology · doi:10.2202/1544-6115.1128 · Cited by 5,684
Self-citationLethality and centrality in protein networks
Jeong, H., Mason, S., Barabási, A., & Oltvai, Z. (2001) · Nature · doi:10.1038/35075138 · Cited by 5,327
The Large-Scale Organization of Metabolic Networks
Jeong, H., Tombor, B., Albert, R., Oltvai, Z. N., & Barabási, A.-L. (2000) · Nature · doi:10.1038/35036627 · Cited by 4,972
Hierarchical Organization of Modularity in Metabolic Networks
Ravasz, E., Somera, A. L., Mongru, D. A., Oltvai, Z. N., & Barabási, A.-L. (2002) · Science · doi:10.1126/science.1073374 · Cited by 4,224
From molecular to modular cell biology.
Hartwell, L. H., Hopfield, J. J., Leibler, S., & Murray, A. W. (1999) · Nature · doi:10.1038/35011540 · Cited by 3,632
R/qtl: QTL mapping in experimental crosses
Broman, K. W., Wu, H., Sen, Ś., & Churchill, G. A. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg112 · Cited by 3,481
Genetic Dissection of Complex Traits
Lander, E. S., & Schork, N. J. (1994) · Science · doi:10.1126/science.8091226 · Cited by 3,425
A Protein Interaction Map of Drosophila melanogaster
Giot, L., Bader, J. S., Brouwer, C., Chaudhuri, A., Kuang, B., Li, Y., Hao, Y. L., Ooi, C. E., Godwin, B., Vitols, E., et al. (2003) · Science · doi:10.1126/science.1090289 · Cited by 1,863
WebGestalt: an integrated system for exploring gene sets in various biological contexts
Zhang, B., Kirov, S. A., & Snoddy, J. R. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki475 · Cited by 1,803
Self-citationEvidence for dynamically organized modularity in the yeast protein–protein interaction network
Han, J. J., Bertin, N., Hao, T., Goldberg, D. S., Berriz, G. F., Zhang, L. V., Dupuy, D., Walhout, A. J. M., Cusick, M. E., Roth, F. P., et al. (2004) · Nature · doi:10.1038/nature02555 · Cited by 1,789
Genetics of gene expression surveyed in maize, mouse and man
Schadt, E. E., Monks, S. A., Drake, T. A., Lusis, A. J., Che, N., Colinayo, V. V., Ruff, T. G., Milligan, S. B., Lamb, J. R., Cavet, G., et al. (2003) · Nature · doi:10.1038/nature01434 · Cited by 1,501
Self-citationReverse engineering of regulatory networks in human B cells
Basso, K., Margolin, A. A., Stolovitzky, G. A., Klein, U., Dalla‐Favera, R., & Califano, A. (2005) · Nature Genetics · doi:10.1038/ng1532 · Cited by 1,408
Genetic Dissection of Transcriptional Regulation in Budding Yeast
Brem, R. B., Yvert, G., Clinton, R., & Kruglyak, L. (2002) · Science · doi:10.1126/science.1069516 · Cited by 1,392
Genetic analysis of genome-wide variation in human gene expression
Morley, M. P., Molony, C. M., Weber, T. M., Devlin, J. L., Ewens, K. G., Spielman, R. S., & Cheung, V. G. (2004) · Nature · doi:10.1038/nature02797 · Cited by 1,212
An integrative genomics approach to infer causal associations between gene expression and disease
Schadt, E. E., Lamb, J., Yang, X., Zhu, J., Edwards, S., GuhaThakurta, D., Sieberts, S. K., Monks, S., Reitman, M., Zhang, C., et al. (2005) · Nature Genetics · doi:10.1038/ng1589 · Cited by 1,043
Self-citationGenetical genomics: the added value from segregation
Jansen, R. (2001) · Trends in Genetics · doi:10.1016/s0168-9525(01)02310-1 · Cited by 1,010
The small world inside large metabolic networks
Wagner, A., & Fell, D. A. (2001) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2001.1711 · Cited by 986
Genomic analysis of regulatory network dynamics reveals large topological changes
Luscombe, N. M., Babu, M. M., Yu, H., Snyder, M. P., Teichmann, S. A., & Gerstein, M. (2004) · Nature · doi:10.1038/nature02782 · Cited by 968
Structure and evolution of transcriptional regulatory networks
Babu, M. M., Luscombe, N. M., Aravind, L., Gerstein, M., & Teichmann, S. A. (2004) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2004.05.004 · Cited by 780
Mouse genetics: concepts and applications
(1995) · Choice Reviews Online · doi:10.5860/choice.33-2135 · Cited by 757
Chesler, E. J., Lu, L., Shou, S., Qu, Y., Gu, J., Wang, J., Hsu, H. C., Mountz, J. D., Baldwin, N. E., Langston, M. A., et al. (2005) · Nature Genetics · doi:10.1038/ng1518 · Cited by 719
Relating Whole-Genome Expression Data with Protein-Protein InteractionsPreprint
Jansen, R., Greenbaum, D. S., & Gerstein, M. (2002) · Genome Research · doi:10.1101/gr.205602 · Cited by 657
A Statistical Framework for Quantitative Trait Mapping
Sen, Ś., & Churchill, G. A. (2001) · Genetics · doi:10.1093/genetics/159.1.371 · Cited by 611
The landscape of genetic complexity across 5,700 gene expression traits in yeast
Brem, R. B., & Kruglyak, L. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0408709102 · Cited by 603
Hübner, N., Wallace, C. A., Zimdahl, H., Petretto, E. G., Schulz, H., MacIver, F. H., Mueller, M., Hummel, O., Monti, J., Zı́dek, V., et al. (2005) · Nature Genetics · doi:10.1038/ng1522 · Cited by 512
Jones, J. R., Barrick, C. J., Kim, K., Lindner, J., Blondeau, B., Fujimoto, Y., Shiota, M., Kesterson, R. A., Kahn, B. B., & Magnuson, M. A. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0306743102 · Cited by 487
Horvath, S., Xu, X. P., Lake, S. L., Silverman, E. K., Weiss, S. T., & Laird, N. M. (2003) · Genetic Epidemiology · doi:10.1002/gepi.10295 · Cited by 391
Self-citationBystrykh, L. V., Weersing, E., Dontje, B., Sutton, S., Pletcher, M. T., Wiltshire, T., Su, A. I., Vellenga, E., Wang, J., Manly, K. F., et al. (2005) · Nature Genetics · doi:10.1038/ng1497 · Cited by 390
Genetic Inheritance of Gene Expression in Human Cell Lines
Monks, S. A., Leonardson, A. S., Zhu, H., Cundiff, P., Pietrusiak, P., Edwards, S. W., Phillips, J. W., Sachs, A. B., & Schadt, E. E. (2004) · The American Journal of Human Genetics · doi:10.1086/426461 · Cited by 356
Self-citationCarlson, M. R. J., Zhang, B., Fang, Z., Mischel, P. S., Horvath, S., & Nelson, S. F. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-40 · Cited by 346
Self-citationCarter, S. L., Brechbühler, C. M., Griffin, M., & Bond, A. T. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth234 · Cited by 344
Hardenbol, P., Yu, F., Belmont, J. W., MacKenzie, J. J., Bruckner, C., Brundage, T., Boudreau, A. A., Chow, S., Eberle, J., Erbilgin, A., et al. (2005) · Genome Research · doi:10.1101/gr.3185605 · Cited by 306
Cis -acting expression quantitative trait loci in mice
Doss, S., Schadt, E. E., Drake, T. A., & Lusis, A. J. (2005) · Genome Research · doi:10.1101/gr.3216905 · Cited by 273
Self-citationAn integrative genomics approach to the reconstruction of gene networks in segregating populations
Zhu, J., Lum, P. Y., Lamb, J., GuhaThakurta, D., Edwards, S. W., Thieringer, R., Berger, J. P., Wu, M. S., Thompson, J., Sachs, A. B., et al. (2004) · Cytogenetic and Genome Research · doi:10.1159/000078209 · Cited by 221
Self-citationSchork, N. J. (1997) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/ajrccm.156.4.12-tac-5 · Cited by 202
Multiple Locus Linkage Analysis of Genomewide Expression in Yeast
Storey, J. D., Akey, J. M., & Kruglyak, L. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030267 · Cited by 195
Hata, K., Nishimura, R., Ikeda, F., Yamashita, K., Matsubara, T., Nokubi, T., & Yoneda, T. (2003) · Molecular Biology of the Cell · doi:10.1091/mbc.e02-06-0356 · Cited by 187
Wrestling with pleiotropy: Genomic and topological analysis of the yeast gene expression network
Featherstone, D. E., & Broadie, K. (2002) · BioEssays · doi:10.1002/bies.10054 · Cited by 179
Wang, S. S.-M., Yehya, N., Schadt, E. E., Wang, H., Drake, T. A., & Lusis, A. J. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020015 · Cited by 178
Self-citationStructure of a large social network
Cśanyi, G., & Szendröi, B. (2004) · Physical Review E · doi:10.1103/physreve.69.036131 · Cited by 151
Combined Expression Trait Correlations and Expression Quantitative Trait Locus Mapping
Hong, L., Chen, M., Flowers, J. B., Yandell, B. S., Stapleton, D. S., Mata, C., Mui, E. T.-K., Flowers, M. T., Schueler, K. L., Manly, K. F., et al. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020006 · Cited by 143
Fins, limbs, and tails: outgrowths and axial patterning in vertebrate evolution
Coates, M. I., & Cohn, M. J. (1998) · BioEssays · doi:10.1002/(sici)1521-1878(199805)20:5 · Cited by 107
Genetical Genomics Analysis of a Yeast Segregant Population for Transcription Network Inference
Bing, N., & Hoeschele, I. (2005) · Genetics · doi:10.1534/genetics.105.041103 · Cited by 106
He, Y. D., Dai, H. A., Schadt, E. E., Cavet, G., Edwards, S. W., Stepaniants, S. B., Duenwald, S., Kleinhanz, R. R., Jones, A. R., Shoemaker, D. D., et al. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg126 · Cited by 90
Self-citationLum, P. Y., Chen, Y., Zhu, J., Lamb, J. R., Melmed, S. K., Wang, S. S.-M., Drake, T. A., Lusis, A. J., & Schadt, E. E. (2006) · Journal of Neurochemistry · doi:10.1111/j.1471-4159.2006.03661.x · Cited by 87
Self-citationGenomic analysis of metabolic pathway gene expression in mice
Ghazalpour, A., Doss, S., Sheth, S. S., Ingram-Drake, L. A., Schadt, E. E., Lusis, A. J., & Drake, T. A. (2005) · Genome biology · doi:10.1186/gb-2005-6-7-r59 · Cited by 84
Self-citationDissection of multigenic obesity traits in congenic mouse strains
Estrada‐Smith, D., Castellani, L. W., Wong, H., Wen, P.-Z., Chui, A., Lusis, A. J., & Davis, R. C. (2004) · Mammalian Genome · doi:10.1007/s00335-003-2294-8 · Cited by 37
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
WGCNA: an R package for weighted correlation network analysis
Langfelder, P., & Horvath, S. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-559 · Cited by 27,252
Self-citationMulti-omics approaches to disease
Hasin, Y., Seldin, M., & Lusis, A. (2017) · Genome Biology · doi:10.1186/s13059-017-1215-1 · Cited by 2,953
Self-citationDefining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R
Langfelder, P., Zhang, B., & Horvath, S. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btm563 · Cited by 1,892
Self-citationGenetics of gene expression and its effect on disease
Emilsson, V., Thorleifsson, G., Zhang, B., Leonardson, A. S., Zink, F., Zhu, J., Carlson, S., Helgason, A., Walters, G. B., Gunnarsdottir, S., et al. (2008) · Nature · doi:10.1038/nature06758 · Cited by 1,296
Self-citationThe transcriptional landscape of polyploid wheat
Ramírez-González, R. H., Borrill, P., Lang, D., Harrington, S. A., Brinton, J., Venturini, L., Davey, M. W., Jacobs, J. J. M. R., Ex, F. V., Pasha, A., et al. (2018) · Science · doi:10.1126/science.aar6089 · Cited by 1,022
Metadata
- Authors
- Ghazalpour, A., Doss, S., Zhang, B., Wang, S., Plaisier, C., Castellanos, R., Brozell, A., Schadt, E. E., Drake, T. A., Lusis, A. J., & Horvath, S.
- Affiliations
- University of California, Los Angeles (US)
- Corresponding author
- Horvath, Steve
- ORCID
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2006-08-18
- Volume
- 2
- Issue
- 8
- Pages
- e130
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- OpenAlex
- W1973651601
- Cited by
- 462
- References
- 52
- Citations by year
- 2026: 5 · 2025: 6 · 2024: 15 · 2023: 14 · 2022: 25 · 2021: 38 · 2020: 27 · 2019: 27 · 2018: 22 · 2017: 14 · 2016: 17 · 2015: 18 · 2014: 20 · 2013: 26 · 2012: 32
- FWCI
- 11.95
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Genetics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- Funders
- National Institutes of Health
- National Heart, Lung, and Blood Institute (HL3 0568, HL28481, P01HL030568, P01HL028481)
- National Human Genome Research Institute (T32HG002536)
- National Institute of General Medical Sciences (T32GM007104, GM08234, GM 07104)
- National Institute of Allergy and Infectious Diseases (U19AI063603)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- mouse body weight, gene co-expression network, gene modules, hepatic gene expression, complex traits, systems biology
- MeSH terms
- Animals, Body Weight, Chromosome Mapping, Crosses, Genetic, Female, Liver, Mice, Inbred C3H, Mice, Inbred C57BL, Models, Genetic, Cluster Analysis, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Gene Expression Profiling, Quantitative Trait Loci, Mice
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
