(1) Gene expression data for genes that we used for this database
(2) Genes in this database with more information and promoter sequenecs
(3) Database tables in SQL format and XML format
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• maize SQL file
• sorghum SQL file
• soybean SQL file
• maize XML file
• sorghum XML file
• soybean XML file
Resources of gene expression data
(1) Maize
(2) Sorghum
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• NCBI SRA: SRP008469 from Davidson RM, et al. Plant Journal. 2012
• NCBI SRA: SRP007361 from Klein, P.E. et al. BMC Genomics. 2011
• NCBI SRA: SRP036640 from Gelli M, et al. BMC Genomics. 2014
(3) Soybean
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• Soybean gene expression atlas from Severin, A.J. et al. BMC Plant Biol 2010
• Soybase
Resources for gene annotations and relevant information
(1) Gene annotations:
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• https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=Zmays
• https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=Gmax
• https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=Sbicolor
• https://www.maizegdb.org/
• https://soybase.org/soyseq/
(2) ePF broswer for maize and soybean:
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• http://bar.utoronto.ca/efp_maize/cgi-bin/efpWeb.cgi?dataSource=Hoopes_et_al_Atlas
• http://bar.utoronto.ca/efpsoybean/cgi-bin/efpWeb.cgi
(3) Orthologue genes of maize, soybean, and sorghum:
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• Orthologue groups in Arabidopsis, soybean, Medicago, Arabidopsis lyrata and Brachypodium https://doi.org/10.1371/journal.pone.0038250.s006 from Jung et al. PLoS One 2012.
• Pan-Grass Syntenic Gene Set: data from Zhang et. al. 2017
References for data sets that were used by this database:
Sekhon, R.S., Briskine, R., Hirsch, C.N., Myers, C.L., Springer, N.M., Buell, C.R., de Leon, N. and Kaeppler, S.M. (2013) Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays. PLoS One, 8, e61005.
Sekhon, R.S., Lin, H., Childs, K.L., Hansey, C.N., Buell, C.R., de Leon, N. and Kaeppler, S.M. (2011) Genome-wide atlas of transcription during maize development. Plant J, 66, 553-563.
Walley, J.W., Sartor, R.C., Shen, Z., Schmitz, R.J., Wu, K.J., Urich, M.A., Nery, J.R., Smith, L.G., Schnable, J.C., Ecker, J.R. et al. (2016) Integration of omic networks in a developmental atlas of maize. Science, 353, 814-818.
Marcon, C., Malik, W.A., Walley, J.W., Shen, Z., Paschold, A., Smith, L.G., Piepho, H.P., Briggs, S.P. and Hochholdinger, F. (2015) A high-resolution tissue-specific proteome and phosphoproteome atlas of maize primary roots reveals functional gradients along the root axes. Plant Physiol, 168, 233-246.
Yu, P., Baldauf, J.A., Lithio, A., Marcon, C., Nettleton, D., Li, C. and Hochholdinger, F. (2016) Root Type-Specific Reprogramming of Maize Pericycle Transcriptomes by Local High Nitrate Results in Disparate Lateral Root Branching Patterns. Plant Physiol, 170, 1783-1798.
Opitz, N., Marcon, C., Paschold, A., Malik, W.A., Lithio, A., Brandt, R., Piepho, H.P., Nettleton, D. and Hochholdinger, F. (2016) Extensive tissue-specific transcriptomic plasticity in maize primary roots upon water deficit. J Exp Bot, 67, 1095-1107.
Makita, Y., Shimada, S., Kawashima, M., Kondou-Kuriyama, T., Toyoda, T. and Matsui, M. (2015) MOROKOSHI: transcriptome database in Sorghum bicolor. Plant Cell Physiol, 56, e6.
Makita, Y., Shimada, S., Kawashima, M., Kondou-Kuriyama, T., Toyoda, T. and Matsui, M. (2015) MOROKOSHI: transcriptome database in Sorghum bicolor. Plant Cell Physiol, 56, e6.
Shakoor, N., Nair, R., Crasta, O., Morris, G., Feltus, A. and Kresovich, S. (2014) A Sorghum bicolor expression atlas reveals dynamic genotype-specific expression profiles for vegetative tissues of grain, sweet and bioenergy sorghums. BMC Plant Biol, 14, 35.
Dugas, D.V., Monaco, M.K., Olsen, A., Klein, R.R., Kumari, S., Ware, D. and Klein, P.E. (2011) Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid. BMC Genomics, 12, 514.
Davidson, R.M., Gowda, M., Moghe, G., Lin, H., Vaillancourt, B., Shiu, S.H., Jiang, N. and Robin Buell, C. (2012) Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution. Plant J, 71, 492-502.
Gelli, M., Duo, Y., Konda, A.R., Zhang, C., Holding, D. and Dweikat, I. (2014) Identification of differentially expressed genes between sorghum genotypes with contrasting nitrogen stress tolerance by genome-wide transcriptional profiling. BMC Genomics, 15, 179.
Grant, D., Nelson, R.T., Cannon, S.B. and Shoemaker, R.C. (2010) SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Res, 38, D843-846.
Severin, A.J., Woody, J.L., Bolon, Y.T., Joseph, B., Diers, B.W., Farmer, A.D., Muehlbauer, G.J., Nelson, R.T., Grant, D., Specht, J.E. et al. (2010) RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome. BMC Plant Biol, 10, 160.