{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,5,22]],"date-time":"2024-05-22T17:40:11Z","timestamp":1716399611981},"reference-count":59,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2014,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>During embryogenesis, signaling molecules produced by one cell population direct gene regulatory changes in neighboring cells and influence their developmental fates and spatial organization. One of the earliest events in the development of the vertebrate embryo is the establishment of three germ layers, consisting of the ectoderm, mesoderm and endoderm. Attempts to measure gene expression<jats:italic>in vivo<\/jats:italic>in different germ layers and cell types are typically complicated by the heterogeneity of cell types within biological samples (i.e., embryos), as the responses of individual cell types are intermingled into an aggregate observation of heterogeneous cell types. Here, we propose a novel method to elucidate gene regulatory circuits from these aggregate measurements in embryos of the frog<jats:italic>Xenopus tropicalis<\/jats:italic>using gene network inference algorithms and then test the ability of the inferred networks to predict spatial gene expression patterns.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We use two inference models with different underlying assumptions that incorporate existing network information, an ODE model for steady-state data and a Markov model for time series data, and contrast the performance of the two models. We apply our method to both control and knockdown embryos at multiple time points to reconstruct the core mesoderm and endoderm regulatory circuits. Those inferred networks are then used in combination with known dorsal-ventral spatial expression patterns of a subset of genes to predict spatial expression patterns for other genes. Both models are able to predict spatial expression patterns for some of the core mesoderm and endoderm genes, but interestingly of different gene subsets, suggesting that neither model is sufficient to recapitulate all of the spatial patterns, yet they are complementary for the patterns that they do capture.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>The presented methodology of gene network inference combined with spatial pattern prediction provides an additional layer of validation to elucidate the regulatory circuits controlling the spatial-temporal dynamics in embryonic development.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1752-0509-8-3","type":"journal-article","created":{"date-parts":[[2014,1,8]],"date-time":"2014-01-08T04:03:04Z","timestamp":1389153784000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns"],"prefix":"10.1186","volume":"8","author":[{"given":"Zhenzhen","family":"Zheng","sequence":"first","affiliation":[]},{"given":"Scott","family":"Christley","sequence":"additional","affiliation":[]},{"given":"William T","family":"Chiu","sequence":"additional","affiliation":[]},{"given":"Ira L","family":"Blitz","sequence":"additional","affiliation":[]},{"given":"Xiaohui","family":"Xie","sequence":"additional","affiliation":[]},{"given":"Ken WY","family":"Cho","sequence":"additional","affiliation":[]},{"given":"Qing","family":"Nie","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2014,1,8]]},"reference":[{"issue":"51","key":"1261_CR1","doi-asserted-by":"publisher","first-page":"20063","DOI":"10.1073\/pnas.0806007105","volume":"105","author":"EH Davidson","year":"2008","unstructured":"Davidson EH, Levine MS: Properties of developmental gene regulatory networks. Proc Natl Acad Sci USA. 2008, 105 (51): 20063-20066. 10.1073\/pnas.0806007105.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"10","key":"1261_CR2","doi-asserted-by":"publisher","first-page":"1010","DOI":"10.1002\/bies.20480","volume":"28","author":"MF Maduro","year":"2006","unstructured":"Maduro MF: Endomesoderm specification in caenorhabditis elegans and other nematodes. Bioessays. 2006, 28 (10): 1010-1022. 10.1002\/bies.20480.","journal-title":"Bioessays"},{"issue":"5881","key":"1261_CR3","doi-asserted-by":"publisher","first-page":"1349","DOI":"10.1126\/science.1158170","volume":"320","author":"L Christiaen","year":"2008","unstructured":"Christiaen L: The transcription\/migration interface in heart precursors of ciona intestinalis. Science. 2008, 320 (5881): 1349-1352. 10.1126\/science.1158170.","journal-title":"Science"},{"issue":"34","key":"1261_CR4","doi-asserted-by":"publisher","first-page":"12763","DOI":"10.1073\/pnas.0604484103","volume":"103","author":"F Biemar","year":"2006","unstructured":"Biemar F: Comprehensive identification of drosophila dorsal-ventral patterning genes using a whole-genome tiling array. Proc Natl Acad Sci USA. 2006, 103 (34): 12763-12768. 10.1073\/pnas.0604484103.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"2","key":"1261_CR5","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1038\/nrg2499","volume":"10","author":"DH Erwin","year":"2009","unstructured":"Erwin DH, Davidson EH: The evolution of hierarchical gene regulatory networks. Nat Rev Genet. 2009, 10 (2): 141-148.","journal-title":"Nat Rev Genet"},{"issue":"2","key":"1261_CR6","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1016\/j.ydbio.2004.04.014","volume":"271","author":"M Loose","year":"2004","unstructured":"Loose M, Patient R: A genetic regulatory network for xenopus mesendoderm formation. Dev Biol. 2004, 271 (2): 467-478. 10.1016\/j.ydbio.2004.04.014.","journal-title":"Dev Biol"},{"issue":"14","key":"1261_CR7","doi-asserted-by":"publisher","first-page":"4943","DOI":"10.1073\/pnas.0408125102","volume":"102","author":"T Koide","year":"2005","unstructured":"Koide T, Hayata T, Cho KW: Xenopus as a model system to study transcriptional regulatory networks. Proc Natl Acad Sci USA. 2005, 102 (14): 4943-4948. 10.1073\/pnas.0408125102.","journal-title":"Proc Natl Acad Sci USA"},{"key":"1261_CR8","doi-asserted-by":"publisher","first-page":"601","DOI":"10.1089\/106652700750050961","volume":"7","author":"N Friedman","year":"2000","unstructured":"Friedman N: Using bayesian networks to analyze expression data. J Comput Biol. 2000, 7: 601-620. 10.1089\/106652700750050961.","journal-title":"J Comput Biol"},{"key":"1261_CR9","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1126\/science.1094068","volume":"303","author":"N Friedman","year":"2004","unstructured":"Friedman N: Inferring cellular networks using probabilistic graphical models. Science. 2004, 303: 799-805. 10.1126\/science.1094068.","journal-title":"Science"},{"issue":"Suppl 2","key":"1261_CR10","doi-asserted-by":"publisher","first-page":"ii138","DOI":"10.1093\/bioinformatics\/btg1071","volume":"19","author":"BE Perrin","year":"2003","unstructured":"Perrin BE: Gene networks inference using dynamic bayesian networks. Bioinformatics. 2003, 19 (Suppl 2): ii138-ii148.","journal-title":"Bioinformatics"},{"issue":"Database issue","key":"1261_CR11","doi-asserted-by":"publisher","first-page":"D866","DOI":"10.1093\/nar\/gkr1050","volume":"40","author":"B Haibe-Kains","year":"2012","unstructured":"Haibe-Kains B: Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks. Nucleic Acids Res. 2012, 40 (Database issue): D866-D875.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"1261_CR12","doi-asserted-by":"publisher","first-page":"e8","DOI":"10.1371\/journal.pbio.0050008","volume":"5","author":"JJ Faith","year":"2007","unstructured":"Faith JJ: Large-scale mapping and validation of escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol. 2007, 5 (1): e8-10.1371\/journal.pbio.0050008.","journal-title":"PLoS Biol"},{"issue":"2","key":"1261_CR13","doi-asserted-by":"publisher","first-page":"662","DOI":"10.1038\/nprot.2006.106","volume":"1","author":"AA Margolin","year":"2006","unstructured":"Margolin AA: Reverse engineering cellular networks. Nat Protoc. 2006, 1 (2): 662-671. 10.1038\/nprot.2006.106.","journal-title":"Nat Protoc"},{"key":"1261_CR14","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1126\/science.1081900","volume":"301","author":"TS Gardner","year":"2003","unstructured":"Gardner TS: Inferring genetic networks and identifying compound mode of action via expression profiling. Science. 2003, 301: 102-105. 10.1126\/science.1081900.","journal-title":"Science"},{"issue":"5","key":"1261_CR15","doi-asserted-by":"publisher","first-page":"R36","DOI":"10.1186\/gb-2006-7-5-r36","volume":"7","author":"R Bonneau","year":"2006","unstructured":"Bonneau R: The inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol. 2006, 7 (5): R36-10.1186\/gb-2006-7-5-r36.","journal-title":"Genome Biol"},{"key":"1261_CR16","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1186\/1752-0509-5-52","volume":"5","author":"R Gupta","year":"2011","unstructured":"Gupta R: A computational framework for gene regulatory network inference that combines multiple methods and datasets. BMC Syst Biol. 2011, 5: 52-10.1186\/1752-0509-5-52.","journal-title":"BMC Syst Biol"},{"issue":"8","key":"1261_CR17","doi-asserted-by":"publisher","first-page":"e6799","DOI":"10.1371\/journal.pone.0006799","volume":"4","author":"S Christley","year":"2009","unstructured":"Christley S, Nie Q, Xie X: Incorporating existing network information into gene network inference. PLoS ONE. 2009, 4 (8): e6799-10.1371\/journal.pone.0006799.","journal-title":"PLoS ONE"},{"issue":"3","key":"1261_CR18","doi-asserted-by":"publisher","first-page":"254","DOI":"10.1109\/TCBB.2005.35","volume":"2","author":"M Gustafsson","year":"2005","unstructured":"Gustafsson M, Hornquist M, Lombardi A: Constructing and analyzing a large-scale gene-to-gene regulatory network\u2013lasso-constrained inference and biological validation. IEEE\/ACM Trans Comput Biol Bioinform. 2005, 2 (3): 254-261. 10.1109\/TCBB.2005.35.","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"issue":"8","key":"1261_CR19","doi-asserted-by":"publisher","first-page":"1626","DOI":"10.1093\/bioinformatics\/bti226","volume":"21","author":"R Guthke","year":"2005","unstructured":"Guthke R: Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection. Bioinformatics. 2005, 21 (8): 1626-1634. 10.1093\/bioinformatics\/bti226.","journal-title":"Bioinformatics"},{"issue":"19","key":"1261_CR20","doi-asserted-by":"publisher","first-page":"2686","DOI":"10.1093\/bioinformatics\/btr454","volume":"27","author":"Z Li","year":"2011","unstructured":"Li Z: Large-scale dynamic gene regulatory network inference combining differential equation models with local dynamic Bayesian network analysis. Bioinformatics. 2011, 27 (19): 2686-2691. 10.1093\/bioinformatics\/btr454.","journal-title":"Bioinformatics"},{"key":"1261_CR21","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1186\/1752-0509-6-6","volume":"6","author":"J Linde","year":"2012","unstructured":"Linde J: Regulatory interactions for iron homeostasis in aspergillus fumigatus inferred by a systems biology approach. BMC Syst Biol. 2012, 6: 6-10.1186\/1752-0509-6-6.","journal-title":"BMC Syst Biol"},{"issue":"1","key":"1261_CR22","doi-asserted-by":"publisher","first-page":"e8121","DOI":"10.1371\/journal.pone.0008121","volume":"5","author":"KY Yip","year":"2010","unstructured":"Yip KY: Improved reconstruction of in silico gene regulatory networks by integrating knockout and perturbation data. PLoS One. 2010, 5 (1): e8121-10.1371\/journal.pone.0008121.","journal-title":"PLoS One"},{"issue":"1","key":"1261_CR23","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1093\/nar\/gkl1001","volume":"35","author":"TT Vu","year":"2007","unstructured":"Vu TT, Vohradsky J: Nonlinear differential equation model for quantification of transcriptional regulation applied to microarray data of saccharomyces cerevisiae. Nucleic Acids Res. 2007, 35 (1): 279-287.","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"1261_CR24","doi-asserted-by":"publisher","first-page":"1154","DOI":"10.1093\/bioinformatics\/bti071","volume":"21","author":"S Kimura","year":"2005","unstructured":"Kimura S: Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm. Bioinformatics. 2005, 21 (7): 1154-1163. 10.1093\/bioinformatics\/bti071.","journal-title":"Bioinformatics"},{"issue":"3","key":"1261_CR25","doi-asserted-by":"publisher","first-page":"846","DOI":"10.1096\/fj.00-0361com","volume":"15","author":"J Vohradsky","year":"2001","unstructured":"Vohradsky J: Neural network model of gene expression. FASEB J. 2001, 15 (3): 846-854. 10.1096\/fj.00-0361com.","journal-title":"FASEB J"},{"issue":"9","key":"1261_CR26","doi-asserted-by":"publisher","first-page":"3468","DOI":"10.1096\/fj.10-160515","volume":"24","author":"CC To","year":"2010","unstructured":"To CC, Vohradsky J: Measurement variation determines the gene network topology reconstructed from experimental data: a case study of the yeast cyclin network. FASEB J. 2010, 24 (9): 3468-3478. 10.1096\/fj.10-160515.","journal-title":"FASEB J"},{"key":"1261_CR27","first-page":"41","volume":"4","author":"P D\u2019Haeseleer","year":"1999","unstructured":"D\u2019Haeseleer P: Linear modeling of mRNA expression levels during CNS development and injury. Pac Symp Biocomput. 1999, 4: 41-52.","journal-title":"Pac Symp Biocomput"},{"issue":"4","key":"1261_CR28","doi-asserted-by":"publisher","first-page":"1693","DOI":"10.1073\/pnas.98.4.1693","volume":"98","author":"NS Holter","year":"2001","unstructured":"Holter NS: Dynamic modeling of gene expression data. Proc Natl Acad Sci USA. 2001, 98 (4): 1693-1698. 10.1073\/pnas.98.4.1693.","journal-title":"Proc Natl Acad Sci USA"},{"key":"1261_CR29","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1089\/10665270252833208","volume":"9","author":"HD Jong","year":"2002","unstructured":"Jong HD: Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol. 2002, 9: 67-103. 10.1089\/10665270252833208.","journal-title":"J Comput Biol"},{"key":"1261_CR30","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1038\/msb4100120","volume":"3","author":"M Bansal","year":"2007","unstructured":"Bansal M: How to infer gene networks from expression profiles. Mol Syst Biol. 2007, 3: 78-","journal-title":"Mol Syst Biol"},{"issue":"11","key":"1261_CR31","doi-asserted-by":"publisher","first-page":"658","DOI":"10.1038\/nchembio.122","volume":"4","author":"R Bonneau","year":"2008","unstructured":"Bonneau R: Learning biological networks: from modules to dynamics. Nat Chem Biol. 2008, 4 (11): 658-664. 10.1038\/nchembio.122.","journal-title":"Nat Chem Biol"},{"issue":"10","key":"1261_CR32","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1038\/nrmicro2419","volume":"8","author":"R De Smet","year":"2010","unstructured":"De Smet R, Marchal K: Advantages and limitations of current network inference methods. Nat Rev Microbiol. 2010, 8 (10): 717-729.","journal-title":"Nat Rev Microbiol"},{"issue":"6","key":"1261_CR33","doi-asserted-by":"publisher","first-page":"2377","DOI":"10.1093\/nar\/gkr902","volume":"40","author":"D Hurley","year":"2012","unstructured":"Hurley D: Gene network inference and visualization tools for biologists: application to new human transcriptome datasets. Nucleic Acids Res. 2012, 40 (6): 2377-2398. 10.1093\/nar\/gkr902.","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"1261_CR34","doi-asserted-by":"publisher","first-page":"796","DOI":"10.1038\/nmeth.2016","volume":"9","author":"D Marbach","year":"2012","unstructured":"Marbach D: Wisdom of crowds for robust gene network inference. Nat Methods. 2012, 9 (8): 796-804. 10.1038\/nmeth.2016.","journal-title":"Nat Methods"},{"key":"1261_CR35","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1186\/1752-0509-4-148","volume":"4","author":"J Linde","year":"2010","unstructured":"Linde J: Regulatory network modelling of iron acquisition by a fungal pathogen in contact with epithelial cells. BMC Syst Biol. 2010, 4: 148-10.1186\/1752-0509-4-148.","journal-title":"BMC Syst Biol"},{"key":"1261_CR36","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1080\/00401706.2000.10485983","volume":"42","author":"AE Hoerl","year":"2000","unstructured":"Hoerl AE, Kennard RW: Ridge regression: biased estimation for nonorthogonal problems. Technometrics. 2000, 42: 80-86. 10.1080\/00401706.2000.10485983. URL: http:\/\/www.jstor.org\/stable\/1271436 10.1080\/00401706.2000.10485983","journal-title":"Technometrics"},{"issue":"2","key":"1261_CR37","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1214\/009053604000000067","volume":"32","author":"B Efron","year":"2004","unstructured":"Efron B: Least angle regression. Ann Stat. 2004, 32 (2): 407-451. 10.1214\/009053604000000067.","journal-title":"Ann Stat"},{"issue":"3","key":"1261_CR38","doi-asserted-by":"publisher","first-page":"432","DOI":"10.1093\/biostatistics\/kxm045","volume":"9","author":"J Friedman","year":"2008","unstructured":"Friedman J, Hastie T, Tibshirani R: Sparse inverse covariance estimation with the graphical lasso. Biostat (Oxford, England). 2008, 9 (3): 432-441. 10.1093\/biostatistics\/kxm045.","journal-title":"Biostat (Oxford, England)"},{"issue":"1","key":"1261_CR39","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1111\/j.2517-6161.1996.tb02080.x","volume":"58","author":"R Tibshirani","year":"1996","unstructured":"Tibshirani R: Regression shrinkage and selection via the lasso. Journal of the royal statistical society. Series B Methodol. 1996, 58 (1): 267-288.","journal-title":"Series B Methodol"},{"key":"1261_CR40","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1111\/j.1467-9868.2005.00503.x","volume":"67","author":"H Zou","year":"2005","unstructured":"Zou H, Hastie T: Regularization and variable selection via the elastic net. J Roy Stat Soc B. 2005, 67: 301-320. 10.1111\/j.1467-9868.2005.00503.x.","journal-title":"J Roy Stat Soc B"},{"key":"1261_CR41","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1038\/msb.2009.102","volume":"6","author":"E Frise","year":"2010","unstructured":"Frise E, Hammonds AS, Celniker SE: Systematic image-driven analysis of the spatial drosophila embryonic expression landscape. Mol Syst Biol. 2010, 6: 345-","journal-title":"Mol Syst Biol"},{"issue":"4","key":"1261_CR42","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1111\/j.1469-7580.2010.01290.x","volume":"217","author":"J Kerwin","year":"2010","unstructured":"Kerwin J: The HUDSEN atlas: a three-dimensional (3D) spatial framework for studying gene expression in the developing human brain. J Anat. 2010, 217 (4): 289-299. 10.1111\/j.1469-7580.2010.01290.x.","journal-title":"J Anat"},{"issue":"9","key":"1261_CR43","doi-asserted-by":"publisher","first-page":"690","DOI":"10.1038\/nrm1979","volume":"7","author":"R Pepperkok","year":"2006","unstructured":"Pepperkok R, Ellenberg J: High-throughput fluorescence microscopy for systems biology. Nat Rev Mol Cell Biol. 2006, 7 (9): 690-696. 10.1038\/nrm1979.","journal-title":"Nat Rev Mol Cell Biol"},{"issue":"2","key":"1261_CR44","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1101\/gr.114595.110","volume":"21","author":"WC Spencer","year":"2011","unstructured":"Spencer WC: A spatial and temporal map of C. elegans gene expression. Genome Res. 2011, 21 (2): 325-341. 10.1101\/gr.114595.110.","journal-title":"Genome Res"},{"issue":"3","key":"1261_CR45","doi-asserted-by":"publisher","first-page":"143","DOI":"10.2976\/1.2907579","volume":"2","author":"J Vermot","year":"2008","unstructured":"Vermot J, Fraser SE, Liebling M: Fast fluorescence microscopy for imaging the dynamics of embryonic development. HFSP J. 2008, 2 (3): 143-155. 10.2976\/1.2907579.","journal-title":"HFSP J"},{"issue":"7","key":"1261_CR46","doi-asserted-by":"publisher","first-page":"e1002589","DOI":"10.1371\/journal.pcbi.1002589","volume":"8","author":"A Crombach","year":"2012","unstructured":"Crombach A: Efficient reverse-engineering of a developmental gene regulatory network. PLoS Comput Biol. 2012, 8 (7): e1002589-10.1371\/journal.pcbi.1002589.","journal-title":"PLoS Comput Biol"},{"issue":"6997","key":"1261_CR47","doi-asserted-by":"publisher","first-page":"368","DOI":"10.1038\/nature02678","volume":"430","author":"J Jaeger","year":"2004","unstructured":"Jaeger J: Dynamic control of positional information in the early drosophila embryo. Nature. 2004, 430 (6997): 368-371. 10.1038\/nature02678.","journal-title":"Nature"},{"issue":"4","key":"1261_CR48","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1016\/S0022-5193(05)80391-1","volume":"152","author":"E Mjolsness","year":"1991","unstructured":"Mjolsness E, Sharp DH, Reinitz J: A connectionist model of development. J Theor Biol. 1991, 152 (4): 429-453. 10.1016\/S0022-5193(05)80391-1.","journal-title":"J Theor Biol"},{"issue":"5","key":"1261_CR49","doi-asserted-by":"publisher","first-page":"e51","DOI":"10.1371\/journal.pcbi.0020051","volume":"2","author":"TJ Perkins","year":"2006","unstructured":"Perkins TJ: Reverse engineering the gap gene network of drosophila melanogaster. PLoS Comput Biol. 2006, 2 (5): e51-10.1371\/journal.pcbi.0020051.","journal-title":"PLoS Comput Biol"},{"key":"1261_CR50","doi-asserted-by":"publisher","first-page":"555","DOI":"10.1186\/1756-0500-5-555","volume":"5","author":"D Botman","year":"2012","unstructured":"Botman D, Kaandorp JA: Spatial gene expression quantification: a tool for analysis of in situ hybridizations in sea anemone nematostella vectensis. BMC Res Notes. 2012, 5: 555-10.1186\/1756-0500-5-555.","journal-title":"BMC Res Notes"},{"issue":"Database issue","key":"1261_CR51","doi-asserted-by":"publisher","first-page":"D607","DOI":"10.1093\/nar\/gkp953","volume":"38","author":"JB Bowes","year":"2010","unstructured":"Bowes JB: Xenbase: gene expression and improved integration. Nucleic Acids Res. 2010, 38 (Database issue): D607-D612.","journal-title":"Nucleic Acids Res"},{"issue":"10","key":"1261_CR52","doi-asserted-by":"publisher","first-page":"1955","DOI":"10.1242\/dev.02358","volume":"133","author":"D Sinner","year":"2006","unstructured":"Sinner D: Global analysis of the transcriptional network controlling xenopus endoderm formation. Development. 2006, 133 (10): 1955-1966. 10.1242\/dev.02358.","journal-title":"Development"},{"issue":"1\u20132","key":"1261_CR53","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1016\/S0925-4773(00)00476-7","volume":"99","author":"D Clements","year":"2000","unstructured":"Clements D, Woodland HR: Changes in embryonic cell fate produced by expression of an endodermal transcription factor, Xsox17. Mech Dev. 2000, 99 (1\u20132): 65-70.","journal-title":"Mech Dev"},{"issue":"6","key":"1261_CR54","doi-asserted-by":"publisher","first-page":"1185","DOI":"10.1016\/j.celrep.2013.08.012","volume":"4","author":"GE Gentsch","year":"2013","unstructured":"Gentsch GE: In vivo T-box transcription factor profiling reveals joint regulation of embryonic neuromesodermal bipotency. Cell Rep. 2013, 4 (6): 1185-1196. 10.1016\/j.celrep.2013.08.012.","journal-title":"Cell Rep"},{"issue":"4","key":"1261_CR55","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1002\/dvdy.10184","volume":"225","author":"MK Khokha","year":"2002","unstructured":"Khokha MK: Techniques and probes for the study of Xenopus tropicalis development. Dev Dyn. 2002, 225 (4): 499-510. 10.1002\/dvdy.10184.","journal-title":"Dev Dyn"},{"issue":"1","key":"1261_CR56","doi-asserted-by":"publisher","first-page":"156","DOI":"10.1016\/0003-2697(87)90021-2","volume":"162","author":"P Chomczynski","year":"1987","unstructured":"Chomczynski P, Sacchi N: Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem. 1987, 162 (1): 156-159.","journal-title":"Anal Biochem"},{"issue":"3","key":"1261_CR57","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1038\/nbt1385","volume":"26","author":"GK Geiss","year":"2008","unstructured":"Geiss GK: Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol. 2008, 26 (3): 317-325. 10.1038\/nbt1385.","journal-title":"Nat Biotechnol"},{"key":"1261_CR58","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1186\/1471-2105-10-262","volume":"10","author":"M Hecker","year":"2009","unstructured":"Hecker M: Integrative modeling of transcriptional regulation in response to antirheumatic therapy. BMC Bioinformatics. 2009, 10: 262-10.1186\/1471-2105-10-262.","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"1261_CR59","doi-asserted-by":"publisher","first-page":"1","DOI":"10.18637\/jss.v033.i01","volume":"33","author":"J Friedman","year":"2010","unstructured":"Friedman J, Hastie T, Tibshirani R: Regularization paths for generalized linear models via coordinate descent. J Stat Softw. 2010, 33 (1): 1-22.","journal-title":"J Stat Softw"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-8-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,22]],"date-time":"2024-05-22T17:14:48Z","timestamp":1716398088000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/1752-0509-8-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,1,8]]},"references-count":59,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2014,12]]}},"alternative-id":["1261"],"URL":"https:\/\/doi.org\/10.1186\/1752-0509-8-3","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,1,8]]},"assertion":[{"value":"16 April 2013","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 December 2013","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 January 2014","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"3"}}