Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells
Open accessAbstract
Background: Recent work has revealed that a core group of transcription factors (TFs) regulates the key characteristics of embryonic stem (ES) cells: pluripotency and self-renewal. Current efforts focus on identifying genes that play important roles in maintaining pluripotency and self-renewal in ES cells and aim to understand the interactions among these genes. To that end, we investigated the use of unsigned and signed network analysis to identify pluripotency and differentiation related genes. Results: We show that signed networks provide a better systems level understanding of the regulatory mechanisms of ES cells than unsigned networks, using two independent murine ES cell expression data sets. Specifically, using signed weighted gene co-expression network analysis (WGCNA), we found a pluripotency module and a differentiation module, which are not identified in unsigned networks. We confirmed the importance of these modules by incorporating genome-wide TF binding data for key ES cell regulators. Interestingly, we find that the pluripotency module is enriched with genes related to DNA damage repair and mitochondrial function in addition to transcriptional regulation. Using a connectivity measure of module membership, we not only identify known regulators of ES cells but also show that Mrpl15, Msh6, Nrf1, Nup133, Ppif, Rbpj, Sh3gl2, and Zfp39, among other genes, have important roles in maintaining ES cell pluripotency and self-renewal. We also report highly significant relationships between module membership and epigenetic modifications (histone modifications and promoter CpG methylation status), which are known to play a role in controlling gene expression during ES cell self-renewal and differentiation. Conclusion: Our systems biologic re-analysis of gene expression, transcription factor binding, epigenetic and gene ontology data provides a novel integrative view of ES cell biology.
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
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?
A signed method creates networks where biologically meaningful modules are better separated than in unsigned networks.
“A signed method creates networks where biologically meaningful modules (such as those representing a specific biological process) are better separated [37].”
From Gene co-expression analysis for functional classification and gene–disease predictions (2017) · cites this paper as [37]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
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 · see citing works
Self-citationTakahashi, K., & Yamanaka, S. (2006) · Cell · doi:10.1016/j.cell.2006.07.024 · Cited by 26,673 · see citing works
Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors
Takahashi, K., Tanabe, K., Ohnuki, M., Narita, M., Ichisaka, T., Tomoda, K., & Yamanaka, S. (2007) · Cell · doi:10.1016/j.cell.2007.11.019 · Cited by 20,221 · see citing works
Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cells
Yu, J., Vodyanik, M. A., Smuga-Otto, K., Antosiewicz-Bourget, J., Frane, J. L., Tian, S., Nie, J., Jonsdottir, G. A., Ruotti, V., Stewart, R., et al. (2007) · Science · doi:10.1126/science.1151526 · Cited by 10,310 · see citing works
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 · see citing works
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 · see citing works
Self-citationA bivalent chromatin structure marks key developmental genes in embryonic stem cells
Bernstein, B. E., Mikkelsen, T. S., Xie, X., Kamal, M., Huebert, D. J., Cuff, J., Fry, B., Meissner, A., Wernig, M., Plath, K., et al. (2006) · Cell · doi:10.1016/j.cell.2006.02.041 · Cited by 5,361 · see citing works
Self-citationHierarchical 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 · see citing works
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.-K., Koche, R. P., et al. (2007) · Nature · doi:10.1038/nature06008 · Cited by 4,129 · see citing works
The Homeoprotein Nanog Is Required for Maintenance of Pluripotency in Mouse Epiblast and ES Cells
Mitsui, K., Tokuzawa, Y., Itoh, H., Segawa, K., Murakami, M., Takahashi, K., Maruyama, M., Maeda, M., & Yamanaka, S. (2003) · Cell · doi:10.1016/s0092-8674(03)00393-3 · Cited by 3,192 · see citing works
Reprogramming of human somatic cells to pluripotency with defined factors
Park, I.-H., Zhao, R., West, J. A., Yabuuchi, A., Huo, H.-G., Ince, T., Lerou, P., Lensch, M., & Daley, G. Q. (2008) · Nature · doi:10.1038/nature06534 · Cited by 3,028 · see citing works
Generation of induced pluripotent stem cells without Myc from mouse and human fibroblasts
Nakagawa, M., Koyanagi, M., Tanabe, K., Takahashi, K., Ichisaka, T., Aoi, T., Okita, K., Mochiduki, Y., Takizawa, N., & Yamanaka, S. (2007) · Nature Biotechnology · doi:10.1038/nbt1374 · Cited by 2,781 · see citing works
Polycomb complexes repress developmental regulators in murine embryonic stem cells
Boyer, L. A., Plath, K., Zeitlinger, J., Brambrink, T., Medeiros, L. A., Lee, T. I., Levine, S. S., Wernig, M., Tajonar, A., Ray, M. K., et al. (2006) · Nature · doi:10.1038/nature04733 · Cited by 2,518 · see citing works
Self-citationChen, X., Han, X., Yuan, P., Fang, F., Huss, M., Vega, V. B., Wong, E., Orlov, Y. L., Zhang, W., Jiang, J., et al. (2008) · Cell · doi:10.1016/j.cell.2008.04.043 · Cited by 2,474 · see citing works
The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells
Loh, Y., Wu, Q., Chew, J.-L., Vega, V. B., Zhang, W., Chen, X., Bourque, G., George, J., Leong, B., Liu, J., et al. (2006) · Nature Genetics · doi:10.1038/ng1760 · Cited by 2,438 · see citing works
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-2003-4-9-r60 · Cited by 2,383 · see citing works
Baines, C. P., Kaiser, R. A., Purcell, N. H., Blair, N. S., Osinska, H., Hambleton, M. A., Brunskill, E. W., Sayen, M. R., Gottlieb, R. A., Dorn, G. W., et al. (2005) · Nature · doi:10.1038/nature03434 · Cited by 2,280 · see citing works
Control of Developmental Regulators by Polycomb in Human Embryonic Stem Cells
Lee, T. I., Jenner, R. G., Boyer, L. A., Guenther, M. G., Levine, S. S., Kumar, R., Chevalier, B. S., Johnstone, S. E., Cole, M. F., Isono, K., et al. (2006) · Cell · doi:10.1016/j.cell.2006.02.043 · Cited by 2,238 · see citing works
A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules
Stuart, J. M., Segal, E., Koller, D., & Kim, S. K. (2003) · Science · doi:10.1126/science.1087447 · Cited by 2,235 · see citing works
Bernstein, B. E., Meissner, A., & Lander, E. S. (2007) · Cell · doi:10.1016/j.cell.2007.01.033 · Cited by 2,086 · see citing works
A Chromatin Landmark and Transcription Initiation at Most Promoters in Human Cells
Guenther, M. G., Levine, S. S., Boyer, L. A., Jaenisch, R., & Young, R. A. (2007) · Cell · doi:10.1016/j.cell.2007.05.042 · Cited by 1,946 · see citing works
Defining 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 · see citing works
Self-citationMaherali, N., Sridharan, R., Xie, W., Utikal, J., Eminli, S., Arnold, K., Stadtfeld, M., Yachechko, R., Tchieu, J., Jaenisch, R., et al. (2007) · Cell stem cell · doi:10.1016/j.stem.2007.05.014 · Cited by 1,725 · see citing works
Self-citationSelective Blockade of MicroRNA Processing by Lin28
Viswanathan, S. R., Daley, G. Q., & Gregory, R. I. (2008) · Science · doi:10.1126/science.1154040 · Cited by 1,442 · see citing works
An Extended Transcriptional Network for Pluripotency of Embryonic Stem Cells
Kim, J., Chu, J., Shen, X., Wang, J., & Orkin, S. H. (2008) · Cell · doi:10.1016/j.cell.2008.02.039 · Cited by 1,321 · see citing works
Embryonic stem cell differentiation: emergence of a new era in biology and medicinePreprint
Keller, G. M. (2005) · Genes & Development · doi:10.1101/gad.1303605 · Cited by 1,144 · see citing works
Generation of human induced pluripotent stem cells from dermal fibroblasts
Lowry, W. E., Richter, L., Yachechko, R., Pyle, A. D., Tchieu, J., Sridharan, R., Clark, A. T., & Plath, K. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0711983105 · Cited by 1,041 · see citing works
Self-citationDissecting self-renewal in stem cells with RNA interference
Ivanova, N., Dobrin, R., Lu, R., Kotenko, I., Levorse, J. M., DeCoste, C. J., Schafer, X., Lun, Y., & Lemischka, I. R. (2006) · Nature · doi:10.1038/nature04915 · Cited by 959 · see citing works
Eigengene networks for studying the relationships between co-expression modules
Langfelder, P., & Horvath, S. (2007) · BMC Systems Biology · doi:10.1186/1752-0509-1-54 · Cited by 867 · see citing works
Self-citationGeometric Interpretation of Gene Coexpression Network Analysis
Horvath, S., & Dong, J. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000117 · Cited by 849 · see citing works
Self-citationFunctional organization of the transcriptome in human brain
Oldham, M. C., Konopka, G., Iwamoto, K., Langfelder, P., Kato, T., Horvath, S., & Geschwind, D. H. (2008) · Nature Neuroscience · doi:10.1038/nn.2207 · Cited by 752 · cited 2× · see citing works
“Gene co-expression network methods have been successfully applied in a variety of different settings [18,19,21,22,24-32].”
BackgroundMethodSelf-citationA core Klf circuitry regulates self-renewal of embryonic stem cells
Jiang, J., Chan, Y.-S., Loh, Y., Cai, J., Tong, G., Lim, C.-A., Robson, P., Zhong, S., & Ng, H. (2008) · Nature Cell Biology · doi:10.1038/ncb1698 · Cited by 746 · see citing works
Horvath, S., Zhang, B., Carlson, M., Lu, K. V., Zhu, S., Felciano, R. M., Laurance, M. F., Zhao, W., Qi, S., Chen, Z., et al. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0608396103 · Cited by 641 · see citing works
Self-citationGene network interconnectedness and the generalized topological overlap measure
Yip, A. M., & Horvath, S. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-22 · Cited by 633 · see citing works
Self-citationConservation and evolution of gene coexpression networks in human and chimpanzee brains
Oldham, M. C., Horvath, S., & Geschwind, D. H. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0605938103 · Cited by 566 · see citing works
Stem-cell-based therapy and lessons from the heart
Passier, R. C., Laake, L. W. V., & Mummery, C. L. (2008) · Nature · doi:10.1038/nature07040 · Cited by 523 · see citing works
Two Supporting Factors Greatly Improve the Efficiency of Human iPSC Generation
Zhao, Y., Yin, X., Qin, H., Zhu, F., Liu, H., Yang, W., Zhang, Q., Xiang, C., Hou, P., Song, Z., et al. (2008) · Cell Stem Cell · doi:10.1016/j.stem.2008.10.002 · Cited by 468 · see citing works
Cho, Y. M., Kwon, S., Pak, Y. K., Seol, H. W., Choi, Y. M., Park, D. J., Park, K. S., & Lee, H. K. (2006) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2006.08.020 · Cited by 465 · see citing works
Integrating Genetic and Network Analysis to Characterize Genes Related to Mouse Weight
Ghazalpour, A., Doss, S., Zhang, B., Wang, S., Plaisier, C., Castellanos, R., Brozell, A., Schadt, E. E., Drake, T. A., Lusis, A. J., et al. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020130 · Cited by 462 · see citing works
Self-citationUnderstanding network concepts in modules
Dong, J., & Horvath, S. (2007) · BMC Systems Biology · doi:10.1186/1752-0509-1-24 · Cited by 455 · see citing works
Self-citationFouse, S. D., Shen, Y., Pellegrini, M. A., Cole, S. W., Meissner, A., Neste, L. V., Jaenisch, R., & Fan, G. (2008) · Cell stem cell · doi:10.1016/j.stem.2007.12.011 · Cited by 452 · see citing works
Self-citationKeller, M. P., Choi, Y., Wang, P., Belt Davis, D., Rabaglia, M. E., Oler, A. T., Stapleton, D. S., Argmann, C., Schueler, K. L., Edwards, S., et al. (2008) · Genome Research · doi:10.1101/gr.074914.107 · Cited by 377 · see citing works
Weighted gene coexpression network analysis strategies applied to mouse weight
Fuller, T. F., Ghazalpour, A., Aten, J. E., Drake, T. A., Lusis, A. J., & Horvath, S. (2007) · Mammalian Genome · doi:10.1007/s00335-007-9043-3 · Cited by 374 · see citing works
Self-citationCathepsin L Proteolytically Processes Histone H3 During Mouse Embryonic Stem Cell Differentiation
Duncan, E. M., Muratore‐Schroeder, T. L., Cook, R. G., Garcia, B. A., Shabanowitz, J., Hunt, D. F., & Allis, C. D. (2008) · Cell · doi:10.1016/j.cell.2008.09.055 · Cited by 364 · see citing works
Regulatory networks define phenotypic classes of human stem cell lines
Müller, F.-J., Laurent, L. C., Kostka, D., Ulitsky, I., Williams, R., Lu, C., Park, I.-H., Rao, M. S., Shamir, R., Schwartz, P. H., et al. (2008) · Nature · doi:10.1038/nature07213 · Cited by 343 · see citing works
Carlson, 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 342 · see citing works
Self-citationCell Cycle Control of Embryonic Stem Cells
White, J., & Dalton, S. (2005) · Stem Cell Reviews and Reports · doi:10.1385/scr:1:2:131 · Cited by 313 · see citing works
Gu, P., Goodwin, B. J., Chung, A. C.-K., Xu, X., Wheeler, D. A., Price, R. R., Galardi, C. M., Peng, L., Latour, A. M., Koller, B. H., et al. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.9.3492-3505.2005 · Cited by 284 · see citing works
A gene regulatory network in mouse embryonic stem cells
Zhou, Q., Chipperfield, H., Melton, D. A., & Wong, W. H. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0701014104 · Cited by 280 · see citing works
Self-citationSaretzki, G. C., Walter, T., Atkinson, S. P., Passos, J. F., Bareth, B., Keith, W. N., Stewart, R., Hoare, S. F., Stojković, M., Armstrong, L., et al. (2007) · Stem Cells · doi:10.1634/stemcells.2007-0628 · Cited by 255 · see citing works
Proteomic analysis of the mouse liver mitochondrial inner membrane
Da Cruz, S., Xenarios, I., Langridge, J., Vilbois, F., Parone, P. A., & Martinou, J.-C. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m304940200 · Cited by 247 · see citing works
Network neighborhood analysis with the multi-node topological overlap measure
Ai, L. S., & Horvath, S. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl581 · Cited by 219 · see citing works
Self-citationTranscriptional Coordination of the Metabolic Network in Arabidopsis
Wei, H., Persson, S., Mehta, T. S., Srinivasasainagendra, V., Chen, L., Page, G. P., Somerville, C. R., & Loraine, A. E. (2006) · PLANT PHYSIOLOGY · doi:10.1104/pp.106.080358 · Cited by 197 · see citing works
Presson, A. P., Sobel, E. M., Papp, J. C., Suarez, C., Whistler, T., Rajeevan, M. S., Vernon, S. D., & Horvath, S. (2008) · BMC Systems Biology · doi:10.1186/1752-0509-2-95 · Cited by 187 · see citing works
Self-citationTranscriptome Analysis of Mouse Stem Cells and Early Embryos
Sharov, A. A., Piao, Y., Matoba, R., Dudekula, D. B., Qian, Y., VanBuren, V., Falco, G., Martin, P. R., Stagg, C. A., Bassey, U. C., et al. (2003) · PLoS Biology · doi:10.1371/journal.pbio.0000074 · Cited by 186 · see citing works
Howard, L., Nelson, K. K., Maciewicz, R. A., & Blobel, C. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.44.31693 · Cited by 180 · see citing works
Nuclear Pore Composition Regulates Neural Stem/Progenitor Cell Differentiation in the Mouse Embryo
Lupu, F. I., Alves, A., Anderson, K. V., Doye, V., & Lacy, E. (2008) · Developmental Cell · doi:10.1016/j.devcel.2008.03.011 · Cited by 172 · see citing works
Lonergan, T. A., Bavister, B. D., & Brenner, C. A. (2007) · Mitochondrion · doi:10.1016/j.mito.2007.05.002 · Cited by 143 · see citing works
Hori, K., Cholewa-Waclaw, J., Nakada, Y., Glasgow, S. M., Masui, T., Henke, R., Wildner, H., Martarelli, B., Beres, T. M., Epstein, J., et al. (2008) · Genes & Development · doi:10.1101/gad.1628008 · Cited by 138 · see citing works
Weston, D. J., Gunter, L. E., Rogers, A., & Wullschleger, S. D. (2008) · BMC Systems Biology · doi:10.1186/1752-0509-2-16 · Cited by 112 · see citing works
Walker, E. M., Ohishi, M., Davey, R. E., Zhang, W. J., Cassar, P. A., Tanaka, T. S., Der, S. D., Morris, Q., Hughes, T. R., Zandstra, P. W., et al. (2007) · Cell stem cell · doi:10.1016/j.stem.2007.04.002 · Cited by 105 · see citing works
Oct4 RNA interference induces trophectoderm differentiation in mouse embryonic stem cells
Velkey, J. M., & O’Shea, K. S. (2003) · genesis · doi:10.1002/gene.10218 · Cited by 102 · see citing works
UTF1 is a chromatin-associated protein involved in ES cell differentiation
van den Boom, V., Kooistra, S. M., Boesjes, M., Geverts, B., Houtsmuller, A. B., Monzen, K., Komuro, I., Essers, J., Drenth-Diephuis, L. J., & Eggen, B. J. L. (2007) · The Journal of Cell Biology · doi:10.1083/jcb.200702058 · Cited by 100 · see citing works
Sakamoto, A., Chen, M., Nakamura, T., Xie, T., Karsenty, G., & Weinstein, L. S. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m500346200 · Cited by 96 · see citing works
Nishimoto, M., Miyagi, S., Yamagishi, T., Sakaguchi, T., Niwa, H., Muramatsu, M., & Okuda, A. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.12.5084-5094.2005 · Cited by 96 · see citing works
Regenerative medicine and human models of human disease
Chien, K. R. (2008) · Nature · doi:10.1038/nature07037 · Cited by 92 · see citing works
An Extended Transcriptional Network for Pluripotency of Embryonic Stem Cells
Kim, J., Chu, J., Shen, X., Wang, J., & Orkin, S. H. (2008) · Cell · doi:10.1016/j.cell.2008.06.004 · Cited by 86 · see citing works
Huang, Y. S., Li, H., Hu, H., Yan, X., Waterman, M. S., Huang, H., & Zhou, X. J. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm222 · Cited by 84 · see citing works
Kendall, S. E., Battelli, C., Irwin, S., Mitchell, J., Glackin, C. A., & Verdi, J. M. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.17.7711-7724.2005 · Cited by 76 · see citing works
Expression and roles of connective tissue growth factor in Meckel's cartilage development
Shimo, T., Kanyama, M., Wu, C., Sugito, H., Billings, P. C., Abrams, W. R., Rosenbloom, J., Iwamoto, M., Pacifici, M., & Koyama, E. (2004) · Developmental Dynamics · doi:10.1002/dvdy.20109 · Cited by 57 · see citing works
Expression of a mouse zinc finger protein gene in both spermatocytes and oocytes during meiosis
Noce, T., Fujiwara, Y., Sezaki, M., Fujimoto, H., & Higashinakagawa, T. (1992) · Developmental Biology · doi:10.1016/0012-1606(92)90120-6 · Cited by 46 · see citing works
Mitochondrial benzodiazepine receptors regulate oxygen homeostasis in the early mouse embryo
O'Hara, M. F., Nibbio, B., Craig, R. C., Rozett, K., Charlap, J. H., & Knudsen, T. B. (2003) · Reproductive Toxicology · doi:10.1016/s0890-6238(03)00035-2 · Cited by 29 · see citing works
Shieh, G. S., Chen, C., Yu, C.-Y., Huang, J., Wang, W.-F., & Lo, Y. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-134 · Cited by 23 · see citing works
Young, L. C., Keuling, A. M., Lai, R. L., Nation, P. N., Tron, V. A., & Andrew, S. E. (2007) · Carcinogenesis · doi:10.1093/carcin/bgm153 · Cited by 23 · see citing works
Bang, A. G., & Carpenter, M. K. (2008) · Science · doi:10.1126/science.1157042 · Cited by 11 · see citing works
A search engine to identify pathway genes from expression data on multiple organisms
Chen, C., Weirauch, M. T., Powell, C. C., Zambon, A. C., & Stuart, J. M. (2007) · BMC Systems Biology · doi:10.1186/1752-0509-1-20 · Cited by 7 · see citing works
Flagged first, then by citations
1 of the 77 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder
Gandal, M. J., Zhang, P., Hadjimichael, E., Walker, R. L., Chen, C., Liu, S., Won, H., van Bakel, H., Varghese, M., Wang, Y., et al. (2018) · Science · doi:10.1126/science.aat8127 · Cited by 1,247 · see citing works
Shared molecular neuropathology across major psychiatric disorders parallels polygenic overlap
Gandal, M. J., Haney, J. R., Parikshak, N. N., Leppa, V., Ramaswami, G., Hartl, C., Schork, A. J., Appadurai, V., Buil, A., Werge, T. M., et al. (2018) · Science · doi:10.1126/science.aad6469 · Cited by 1,095 · see citing works
Self-citationGene co-expression analysis for functional classification and gene–disease predictions
van Dam, S., Võsa, U., van der Graaf, A., Franke, L., & de Magalhães, J. P. (2017) · Briefings in Bioinformatics · doi:10.1093/bib/bbw139 · Cited by 1,086 · see citing works
Is My Network Module Preserved and Reproducible?
Langfelder, P., Luo, R., Oldham, M. C., & Horvath, S. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1001057 · Cited by 1,012 · see citing works
Self-citationCorrelating transcriptional networks to breast cancer survival: a large-scale coexpression analysis
Clarke, C., Madden, S. F., Doolan, P., Aherne, S. T., Joyce, H., O’Driscoll, L., Gallagher, W. M., Hennessy, B. T., Moriarty, M. J., Crown, J. P., et al. (2013) · Carcinogenesis · doi:10.1093/carcin/bgt208 · Cited by 849 · see citing works
Rare coding variants in the phospholipase D3 gene confer risk for Alzheimer’s disease
Cruchaga, C., Karch, C. M., Jin, S. C., Benitez, B. A., Cai, Y., Guerreiro, R., Harari, O., Norton, J., Budde, J., Bertelsen, S., et al. (2014) · Nature · doi:10.1038/nature12825 · Cited by 461 · see citing works
Comparison of co-expression measures: mutual information, correlation, and model based indices
Song, L., Langfelder, P., & Horvath, S. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-328 · Cited by 460 · see citing works
Self-citationThe nuclear envelope environment and its cancer connections
Chow, K.-H., Factor, R. E., & Ullman, K. S. (2012) · Nature reviews. Cancer · doi:10.1038/nrc3219 · Cited by 361 · see citing works
When is hub gene selection better than standard meta-analysis?
Langfelder, P., Mischel, P. S., & Horvath, S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0061505 · Cited by 313 · see citing works
Self-citationTanaka, H., Kono, E. A., Tran, C. P., Miyazaki, H., Yamashiro, J. M., Shimomura, T., Fazli, L., Wada, R., Huang, J., Vessella, R. L., et al. (2010) · Nature Medicine · doi:10.1038/nm.2236 · Cited by 340 · see citing works
Self-citationMechanisms of Severe Acute Respiratory Syndrome Coronavirus-Induced Acute Lung Injury
Gralinski, L. E., Bankhead, A., Jeng, S., Menachery, V. D., Proll, S. C., Belisle, S. E., Matzke, M. M., Webb‐Robertson, B., Luna, M. L., Shukla, A. K., et al. (2013) · mBio · doi:10.1128/mbio.00271-13 · Cited by 310 · see citing works
The Biotrophic Development of Ustilago maydis Studied by RNA-Seq Analysis
Lanver, D., Müller, A. N., Happel, P., Schweizer, G., Haas, F. B., Franitza, M., Pellegrin, C., Reißmann, S., Altmüller, J., Rensing, S. A., et al. (2018) · The Plant Cell · doi:10.1105/tpc.17.00764 · Cited by 236 · see citing works
Yu, Q., Erhardt, E. B., Jing Sui （Beijing Normal University）， my correct affiliation is beijing normal university, N. Q. U. O. S. A. T., Du, Y., He, H., Hjelm, D., Cetin, M. S., Rachakonda, S., Miller, R. L., Pearlson, G. D., et al. (2014) · NeuroImage · doi:10.1016/j.neuroimage.2014.12.020 · Cited by 232 · see citing works
Insights into TREM2 biology by network analysis of human brain gene expression data
Forabosco, P., Ramasamy, A., Trabzuni, D., Walker, R., Smith, C., Bras, J., Levine, A. P., Hardy, J., Pocock, J. M., Guerreiro, R., et al. (2013) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2013.05.001 · Cited by 180 · see citing works
Shared Molecular Neuropathology Across Major Psychiatric Disorders Parallels Polygenic Overlap
Gandal, M. J., Haney, J. R., Parikshak, N., Leppä, V., Ramaswami, G., Hartl, C., Schork, A. J., Appadurai, V., Buil, A., Werge, T. M., et al. (2019) · FOCUS The Journal of Lifelong Learning in Psychiatry · doi:10.1176/appi.focus.17103 · Cited by 209 · see citing works
Comparing Statistical Methods for Constructing Large Scale Gene Networks
Allen, J. D., Xie, Y., Chen, M., Girard, L., & Xiao, G. (2012) · PLoS ONE · doi:10.1371/journal.pone.0029348 · Cited by 186 · see citing works
Modeling Host Genetic Regulation of Influenza Pathogenesis in the Collaborative Cross
Ferris, M. T., Aylor, D. L., Bottomly, D., Whitmore, A. C., Aicher, L. D., Bell, T. A., Bradel-Tretheway, B., Bryan, J. T., Buus, R. J., Gralinski, L. E., et al. (2013) · PLoS Pathogens · doi:10.1371/journal.ppat.1003196 · Cited by 186 · see citing works
Oldham, M. C., Langfelder, P., & Horvath, S. (2012) · BMC Systems Biology · doi:10.1186/1752-0509-6-63 · Cited by 154 · see citing works
Self-citationPriming of microglia in a DNA-repair deficient model of accelerated aging
Raj, D. D. A., Jaarsma, D., Holtman, I. R., Olah, M., Ferreira, F. M., Schaafsma, W., Brouwer, N., Meijer, M., de Waard, M. C., van der Pluijm, I., et al. (2014) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2014.03.025 · Cited by 144 · see citing works
Schmidt, F., Gasparoni, N., Gasparoni, G., Gianmoena, K., Cadenas, C., Polansky, J. K., Ebert, P., Nordström, K. J. V., Barann, M., Sinha, A. N., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1061 · Cited by 118 · see citing works
GeneFriends: a human RNA-seq-based gene and transcript co-expression database
van Dam, S., Craig, T., & de Magalhães, J. P. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1042 · Cited by 115 · see citing works
Is human blood a good surrogate for brain tissue in transcriptional studies?
Cai, C., Langfelder, P., Fuller, T. F., Oldham, M. C., Luo, R., van den Berg, L. H., Ophoff, R. A., & Horvath, S. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-589 · Cited by 122 · see citing works
Self-citationChen, L., Yuan, L., Wang, Y., Wang, G., Zhu, Y., Cao, R., Qian, G., Xie, C., Liu, X., Xiao, Y., et al. (2017) · International Journal of Biological Sciences · doi:10.7150/ijbs.21657 · Cited by 118 · see citing works
Lukoseviciute, M., Gavriouchkina, D., Williams, R. M., Hochgreb-Hagele, T., Senanayake, U., Chong-Morrison, V., Thongjuea, S., Repapi, E., Mead, A., & Sauka-Spengler, T. (2018) · Developmental Cell · doi:10.1016/j.devcel.2018.11.009 · Cited by 109 · see citing works
Liu, B., Yu, H., Tu, K., Li, C., Li, Y., & Li, Y. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq471 · Cited by 112 · see citing works
Kuegler, P. B. (2010) · ALTEX · doi:10.14573/altex.2010.1.16 · Cited by 109 · see citing works
Link-based quantitative methods to identify differentially coexpressed genes and gene Pairs
Yu, H., Liu, B., Ye, Z., Li, C., Li, Y., & Li, Y. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-315 · Cited by 104 · see citing works
Newman, A. M., & Cooper, J. B. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-117 · Cited by 104 · see citing works
Liu, J., Zhou, S., Li, S., Jiang, Y., Wan, Y., Ma, X., & Cheng, W. (2019) · Cancer Cell International · doi:10.1186/s12935-019-0859-1 · Cited by 100 · see citing works
DCGL v2.0: An R Package for Unveiling Differential Regulation from Differential Co-expression
Yang, J., Yu, H., Liu, B., Zhao, Z., Liu, L., Ma, L., Li, Y., & Li, Y. (2013) · PLoS ONE · doi:10.1371/journal.pone.0079729 · Cited by 98 · see citing works
Yu, Q., Plis, S., Erhardt, E. B., Allen, E. A., Jing Sui （Beijing Normal University）， my correct affiliation is beijing normal university, N. Q. U. O. S. A. T., Kiehl, K. A., Pearlson, G. D., & Calhoun, V. D. (2012) · Frontiers in Systems Neuroscience · doi:10.3389/fnsys.2011.00103 · Cited by 91 · see citing works
Liu, J., Jing, L., & Tu, X. (2016) · BMC Cardiovascular Disorders · doi:10.1186/s12872-016-0217-3 · Cited by 89 · see citing works
Detecting network modules in fMRI time series: A weighted network analysis approach
Mumford, J. A., Horvath, S., Oldham, M. C., Langfelder, P., Geschwind, D. H., & Poldrack, R. A. (2010) · NeuroImage · doi:10.1016/j.neuroimage.2010.05.047 · Cited by 81 · see citing works
Self-citationBakhtiarizadeh, M. R., Hosseinpour, B., Shahhoseini, M., Korte, A., & Gifani, P. (2018) · Frontiers in Genetics · doi:10.3389/fgene.2018.00453 · Cited by 78 · see citing works
Yuan, L., Zeng, G., Chen, L., Wang, G., Wang, X., Cao, X., Lü, M., Liu, X., Qian, G., Xiao, Y., et al. (2018) · International Journal of Biological Sciences · doi:10.7150/ijbs.23574 · Cited by 76 · see citing works
Clarke, C., Doolan, P., Barron, N., Meleady, P., O’Sullivan, F., Gammell, P., Melville, M. W., Leonard, M. W., & CLYNES, M. M. (2011) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2011.07.011 · Cited by 74 · see citing works
Mamdani, M., Williamson, V., McMichael, G. O., Blevins, T., Aliev, F., Adkins, A., Hack, L., Bigdeli, T., D. van der Vaart, A., Web, B. T., et al. (2015) · PLOS ONE · doi:10.1371/journal.pone.0137671 · Cited by 73 · see citing works
Levine, A. J., Miller, J. A., Shapshak, P., Gelman, B. B., Singer, E. J., Hinkin, C. H., Commins, D., Morgello, S., Grant, I., & Horvath, S. (2013) · BMC Medical Genomics · doi:10.1186/1755-8794-6-4 · Cited by 72 · see citing works
Self-citationHorvath, S., Nazmul-Hossain, A. N. M., Pollard, R., Kroese, F. G. M., Vissink, A., Kallenberg, C. G. M., Spijkervet, F. K., Bootsma, H., Michie, S. A., Gorr, S., et al. (2012) · Arthritis Research & Therapy · doi:10.1186/ar4081 · Cited by 71 · see citing works
Self-citationHistone proteolysis: A proposal for categorization into ‘clipping’ and ‘degradation’
Dhaenens, M., Glibert, P., Meert, P., Vossaert, L., & Deforce, D. L. D. (2014) · BioEssays · doi:10.1002/bies.201400118 · Cited by 69 · see citing works
Systems biology of ovine intestinal parasite resistance: disease gene modules and biomarkers
Kadarmideen, H. N., Watson‐Haigh, N. S., & Andronicos, N. M. (2010) · Molecular BioSystems · doi:10.1039/c0mb00190b · Cited by 66 · see citing works
Gene differential coexpression analysis based on biweight correlation and maximum clique
Zheng, C.-H., Yuan, L., Sha, W., & Sun, Z.-L. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-s15-s3 · Cited by 65 · see citing works
Histone demethylase KDM2A promotes tumor cell growth and migration in gastric cancer
Huang, Y., Liu, Y., Yu, L., Chen, J., Hou, J., Cui, L., Ma, D., & Wang-kun, L. (2014) · Tumor Biology · doi:10.1007/s13277-014-2630-5 · Cited by 63 · see citing works
Gysi, D. M., Voigt, A., Fragoso, T. D. M., Almaas, E., & Nowick, K. (2018) · NORA - Norwegian Open Research Archives · doi:10.17169/refubium-922 · Cited by 62 · see citing works
Hasankhani, A., Bahrami, A., Sheybani, N., Aria, B., Hemati, B., Fatehi, F., Farahani, H. G. M., Javanmard, G., Rezaee, M., Kastelic, J. P., et al. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.789317 · Cited by 61 · see citing works
Walsh, C. J., Batt, J. A. E., Herridge, M. S., Mathur, S., Bader, G. D., Hu, P., & dos Santos, C. C. (2016) · Scientific Reports · doi:10.1038/srep29334 · Cited by 58 · see citing works
Wu, Z., Wang, L., Wen, Z., & Yao, J. (2021) · Scientific Reports · doi:10.1038/s41598-021-82976-w · Cited by 59 · see citing works
Improved biomarker discovery through a plot twist in transcriptomic data analysis
Sánchez-Baizán, N., Ribas, L., & Piferrer, F. (2022) · BMC Biology · doi:10.1186/s12915-022-01398-w · Cited by 60 · see citing works
Menachery, V. D., & Baric, R. S. (2013) · Immunological Reviews · doi:10.1111/imr.12092 · Cited by 57 · see citing works
Huggett, S. B., & Stallings, M. C. (2019) · Addiction Biology · doi:10.1111/adb.12719 · Cited by 53 · see citing works
Epigenetic modulation of brain gene networks for cocaine and alcohol abuse
Farris, S. P., Harris, R. A., & Ponomarev, I. (2015) · Frontiers in Neuroscience · doi:10.3389/fnins.2015.00176 · Cited by 57 · see citing works
Gysi, D. M., Voigt, A., Fragoso, T. D. M., Almaas, E., & Nowick, K. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2351-7 · Cited by 70 · see citing works
Shi, K., Bing, Z., Cao, G.-Q., Guo, L., Cao, Y., Jiang, H., & Zhang, M. (2015) · Europe PMC (PubMed Central) · doi:10.3980/j.issn.2222-3959.2015.02.10 · Cited by 56 · see citing works
Zhang, J., & Huang, K. (2014) · Cancer Informatics · doi:10.4137/cin.s14021 · Cited by 54 · see citing works
Rigidity and flexibility of biological networks
Gaspar, M. E., & Csermely, P. (2012) · Briefings in Functional Genomics · doi:10.1093/bfgp/els023 · Cited by 52 · see citing works
He, Y., Wang, Z., Ge, H., Liu, Y., & Chen, H. (2021) · Plant Science · doi:10.1016/j.plantsci.2021.110935 · Cited by 51 · see citing works
Yu, Q., Du, Y., Chen, J., He, H., Jing Sui （Beijing Normal University）， my correct affiliation is beijing normal university, N. Q. U. O. S. A. T., Pearlson, G. D., & Calhoun, V. D. (2017) · Journal of Neuroscience Methods · doi:10.1016/j.jneumeth.2017.08.007 · Cited by 50 · see citing works
Bai, Y., Xiong, L., Zhu, M., Yang, Z., Zhao, J., & Tang, H. (2019) · Cancer Biomarkers · doi:10.3233/cbm-181512 · Cited by 50 · see citing works
MRPL15 is a novel prognostic biomarker and therapeutic target for epithelial ovarian cancer
Xu, H., Zou, R., Li, F., Liu, J., Luan, N., Wang, S., & Zhu, L. (2021) · Cancer Medicine · doi:10.1002/cam4.3907 · Cited by 49 · see citing works
Troy, N. M., Hollams, E. M., Holt, P. G., & Bosco, A. (2016) · BMC Medical Genomics · doi:10.1186/s12920-016-0171-z · Cited by 49 · see citing works
Huang, Y. H., Xu, Y., Lu, Y., Zhu, S., Guo, Y., Sun, C., Xu, L., Chen, X., Zhao, Y., Yu, B., et al. (2019) · Biomaterials · doi:10.1016/j.biomaterials.2019.119266 · Cited by 43 · see citing works
Wang, T., Zheng, X., Li, R., Liu, X., Wu, J., Zhong, X., Zhang, W., Liu, Y., He, X., Liu, W., et al. (2018) · Journal of Cellular Physiology · doi:10.1002/jcp.27381 · Cited by 42 · see citing works
attract: A Method for Identifying Core Pathways That Define Cellular Phenotypes
Mar, J. C., Matigian, N., Quackenbush, J. F., & Wells, C. A. (2011) · PLoS ONE · doi:10.1371/journal.pone.0025445 · Cited by 40 · see citing works
Meta-analysis of drought-tolerant genotypes in Oryza sativa: A network-based approach
Sircar, S., & Parekh, N. (2019) · PLoS ONE · doi:10.1371/journal.pone.0216068 · Cited by 43 · see citing works
Basnet, R. K., Moreno-Pachon, N. M., Lin, K., Bucher, J., Visser, R. G. F., Maliepaard, C. A., & Bonnema, G. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-840 · Cited by 39 · see citing works
Zhou, Z., Liu, S., Zhang, M., Zhou, R., Liu, J., Chang, Y., & Zhao, Q. (2017) · Digestive Diseases and Sciences · doi:10.1007/s10620-017-4718-4 · Cited by 39 · see citing works
Protein expression based multimarker analysis of breast cancer samples
Presson, A. P., Yoon, N. K., Bagryanova, L., Mah, V. H., Alavi, M., Maresh, E. L., Rajasekaran, A. K., Goodglick, L., Chia, D., & Horvath, S. (2011) · BMC Cancer · doi:10.1186/1471-2407-11-230 · Cited by 38 · see citing works
Self-citationWang, F., Chang, Y., Li, J., Wang, H., Zhou, R., Qi, J., Liu, J., & Zhao, Q. (2016) · Digestive and Liver Disease · doi:10.1016/j.dld.2016.10.017 · Cited by 38 · see citing works
Xia, M., Yu, R., & Chen, D. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2021.809325 · Cited by 38 · see citing works
Stochastic block model and exploratory analysis in signed networks
Jiang, J. Q. (2015) · Physical Review E · doi:10.1103/physreve.91.062805 · Cited by 37 · see citing works
Overlapping community detection in networks with positive and negative links
Chen, Y., Wang, X. L., Yuan, B., & Tang, B. Z. (2014) · Journal of Statistical Mechanics Theory and Experiment · doi:10.1088/1742-5468/2014/03/p03021 · Cited by 36 · see citing works
Inferring interaction type in gene regulatory networks using co-expression data
Khosravi, P., Gazestani, V., Pirhaji, L., Law, B., Sadeghi, M., Goliaei, B., & Bader, G. D. (2015) · Algorithms for Molecular Biology · doi:10.1186/s13015-015-0054-4 · Cited by 36 · see citing works
Antigen-stimulated PBMC transcriptional protective signatures for malaria immunization
Moncunill, G., Scholzen, A., Mpina, M., Nhabomba, A. J., Hounkpatin, A. B., Osaba, L., Valls, R., Campo, J. J., Sanz, H., Jairoce, C., et al. (2020) · Science Translational Medicine · doi:10.1126/scitranslmed.aay8924 · Cited by 36 · see citing works
Huang, H., Zhang, Q., Ye, C., Lv, J.-M., Liu, X., Chen, L., Wu, H., Yin, L., Cui, X., Xu, D.-F., et al. (2017) · Journal of Cancer Research and Clinical Oncology · doi:10.1007/s00432-017-2497-0 · Cited by 35 · see citing works
Jahagirdar, S., & Saccenti, E. (2020) · Metabolites · doi:10.3390/metabo10040171 · Cited by 32 · see citing works
Insights into the Ecology and Evolution of Polyploid Plants through Network Analysis
Gallagher, J. P., Grover, C. E., Hu, G., & Wendel, J. F. (2016) · Molecular Ecology · doi:10.1111/mec.13626 · Cited by 31 · see citing works
SpaceX: gene co-expression network estimation for spatial transcriptomics
Acharyya, S., Zhou, X., & Baladandayuthapani, V. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac645 · Cited by 32 · see citing works
Protein co-expression network analysis (ProCoNA)
Gibbs, D. L., Baratt, A., Baric, R. S., Kawaoka, Y., Smith, R. D., ORWOLL, E. S., Katze, M. G., & McWeeney, S. K. (2013) · Journal of Clinical Bioinformatics · doi:10.1186/2043-9113-3-11 · Cited by 29 · see citing works
Stochastic Blockmodeling and Variational Bayes Learning for Signed Network Analysis
Yang, B. X., Liu, X., Li, Y., & Zhao, X. (2017) · IEEE Transactions on Knowledge and Data Engineering · doi:10.1109/tkde.2017.2700304 · Cited by 31 · see citing works
Functional Modules Distinguish Human Induced Pluripotent Stem Cells from Embryonic Stem Cells
Wang, A., Huang, K. Y., Shen, Y., Xue, Z., Cai, C., Horvath, S., & Fan, G. (2011) · Stem Cells and Development · doi:10.1089/scd.2010.0574 · Cited by 30 · see citing works
Self-citationVoigt, E. A., Grill, D. E., Zimmermann, M. T., Simon, W. L., Ovsyannikova, I. G., Kennedy, R. B., & Poland, G. A. (2018) · Scientific Reports · doi:10.1038/s41598-017-17735-x · Cited by 30 · see citing works
Chen, P., Wang, F., Nie, J.-Y., Feng, J., Liu, J., Zhou, R., Wang, H., & Zhao, Q. (2018) · OncoTargets and Therapy · doi:10.2147/ott.s176511 · Cited by 30 · see citing works
Yuan, L., Chen, L., Qian, K., Wang, G., Lü, M., Qian, G., Cao, X., Jiang, W., Xiao, Y., & Wang, X. (2017) · Oncology Reports · doi:10.3892/or.2017.6132 · Cited by 29 · see citing works
Gómez, J. C. I., & Orgueira, A. M. (2014) · Frontiers in Oncology · doi:10.3389/fonc.2014.00147 · Cited by 28 · see citing works
Xiong, Y., Yuan, L., Chen, L., Zhu, Y., Zhang, S., Liu, X., Xiao, Y., & Wang, X. (2018) · Journal of Cancer · doi:10.7150/jca.25900 · Cited by 28 · see citing works
Kim, A., Yoon, D., Lim, Y., Roh, H., Kim, S., Park, C., Kim, H., Cha, H., Choi, Y. H., & Kim, D. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21051707 · Cited by 26 · see citing works
Wang, H., Wang, F., Chen, P., Zhang, M., Yu, M., Wang, H., Zhao, Q., & Liu, J. (2019) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2018.12.135 · Cited by 27 · see citing works
Yazdi, P. G., Su, H., Ghimbovschi, S. D., Fan, W., Coskun, P. E., Nalbandian, A., Knoblach, S. M., Resnick, J. L., Hoffman, E. P., Wallace, D. C., et al. (2013) · Clinical and Translational Science · doi:10.1111/cts.12083 · Cited by 27 · see citing works
An update on clonality: what smooth muscle cell type makes up the atherosclerotic plaque?
Schwartz, S. M., Virmani, R., & Majesky, M. W. (2018) · F1000Research · doi:10.12688/f1000research.15994.1 · Cited by 27 · see citing works
Chen, P., Long, B., Xu, Y., Wu, W., & Zhang, S. (2018) · Frontiers in Physiology · doi:10.3389/fphys.2018.01778 · Cited by 26 · see citing works
Chen, Y., Bi, F., An, Y., & Yang, Q. F. (2018) · Journal of Cellular Biochemistry · doi:10.1002/jcb.27567 · Cited by 25 · see citing works
Hasankhani, A., Bahrami, A., Sheybani, N., Fatehi, F., Abadeh, R., Farahani, H. G. M., Behzadi, M. R. B., Javanmard, G., Isapour, S., Khadem, H., et al. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.753839 · Cited by 27 · see citing works
Multi-omic network signatures of disease
Gibbs, D. L., Gralinski, L. E., Baric, R. S., & McWeeney, S. K. (2014) · Frontiers in Genetics · doi:10.3389/fgene.2013.00309 · Cited by 26 · see citing works
Genetic architecture of gene expression in ovine skeletal muscle
Kogelman, L. J. A., Byrne, K. A., Vuocolo, T., Watson‐Haigh, N. S., Kadarmideen, H. N., Kijas, J., Oddy, V. H., Gardner, G. E., Gondro, C., & Tellam, R. L. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-607 · Cited by 25 · see citing works
Wang, W., Fu, S., Lin, X., Zheng, J., Pu, J., Gu, Y., Deng, W., Liu, Y., He, Z., Liang, W., et al. (2019) · OncoTargets and Therapy · doi:10.2147/ott.s220823 · Cited by 25 · see citing works
Levine, A. J., Horvath, S., Miller, E. N., Singer, E. J., Shapshak, P., Baldwin, G. C., Martı́nez-Maza, O., Witt, M. D., & Langfelder, P. (2013) · Journal of Neuroimmunology · doi:10.1016/j.jneuroim.2013.09.016 · Cited by 24 · see citing works
Self-citationAn evolutionary game approach for determination of the structural conflicts in signed networks
Tan, S., & Lü, J. (2016) · Scientific Reports · doi:10.1038/srep22022 · Cited by 24 · see citing works
Knockdown of CENPF inhibits the progression of lung adenocarcinoma mediated by ERβ2/5 pathway
Hexiao, T., Yuquan, B., Xiong, L., Wei, Y., Li, S., Hu, W., Xu, M., Xuefeng, Z., Gaofeng, P., Li, Z., et al. (2021) · Aging · doi:10.18632/aging.202303 · Cited by 24 · see citing works
Toward a complete in silico , multi‐layered embryonic stem cell regulatory network
Xu, H., Schaniel, C., Lemischka, I. R., & Ma’ayan, A. (2010) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.93 · Cited by 24 · see citing works
PoLoBag: Polynomial Lasso Bagging for signed gene regulatory network inference from expression data
Roy, G. G., Geard, N. L., Verspoor, K. M., & He, S. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa651 · Cited by 22 · see citing works
- Authors
- Mason, M. J., Fan, G., Plath, K., Zhou, Q., & Horvath, S.
- Affiliations
- University of California, Los Angeles (US)
- Corresponding author
- Zhou, Qing
- Horvath, Steve
- Venue
- BMC Genomics
- Published
- 2009-07-20
- Volume
- 10
- Issue
- 1
- Pages
- 327-327
- ISSN
- 1471-2164 (ISSN-L)
- PMC
- PMC2727539
- OpenAlex
- W2138720219
- Cited by
- 243
- References
- 77
- Citations by year
- 2026: 8 · 2025: 10 · 2024: 12 · 2023: 12 · 2022: 18 · 2021: 34 · 2020: 18 · 2019: 18 · 2018: 18 · 2017: 12 · 2016: 10 · 2015: 8 · 2014: 14 · 2013: 22 · 2012: 11
- FWCI
- 3.89
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- BMC Genomics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- The HKU Scholars Hub (University of Hong Kong) (submittedVersion)
- Funders
- National Science Foundation (0805491)
- National Institutes of Health (1dp2od001686-01)
- National Cancer Institute (P50CA092131, P30CA016042)
- National Institute of General Medical Sciences (P01GM081621)
- National Institute of Allergy and Infectious Diseases (U19AI063603)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK072206, DK-072206)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Pluripotent Stem Cells Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- mouse embryonic stem cells, pluripotency, self-renewal, gene co-expression network, transcriptional regulation, transcription factor binding, DNA repair, mitochondrial function, histone modifications, promoter CpG methylation, epigenetic regulation, module membership
- MeSH terms
- Animals, Chromatin, DNA, DNA Damage, DNA Repair, Gene Expression Regulation, Protein Binding, Transcription Factors, Transcription, Genetic, CpG Islands, DNA Methylation, Gene Expression Profiling, Pluripotent Stem Cells, Mice, Gene Regulatory Networks, Embryonic Stem Cells
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
