Expression Experimental Design: Expression data from various tomato plant tissues

Experimental Design Basic Information 
Experimental design name: Expression data from various tomato plant tissues
Experimental design type: Multiple Comparisson
Description: Gene-to-gene coexpression analysis is a powerful approach to infer function of uncharacterized genes. To perform non-targeted coexpression analysis of tomato genes, we collected a developmental gene expression dataset using various tissues of tomato plant. Expression data are collected from 24 different tissue types including root, hypocotyl, cotyledon, leaf at different stages, and fruit tissues at 4 different ripening stages from 4 different Solanum lycopersicum cultivars. Fruits were separated to the flesh and the peel. These two tissue types indeed showed remarkably different gene expression profiles. We also collected data from 4 different ripening stages (mature green, yellow, orange, and red) to detail the changes during ripening. By using this gene expression dataset, we calculated pair-wise Pearson s correlation coefficients, and performed network-based coexpression analysis. The analysis generated a number of coexpression modules, some of which showed an enrichment of genes associated with specific functional categories. This result will be useful in inferring functions of uncharacterized tomato genes, and in prioritizing genes for further experimental analysis. We used Affymetrix GeneChip Tomato genome Arrays to detail the global gene expression change using 24 different tomato tissue types (67 hybridizations). We collected gene expression data from 24 different tomato tissue types using 67 hybridizations. Root, hypocotyl, cotyledon, and leaf were sampled from 3-week-old or 5-week old plant of Solanum lycopersicum cultivar Micro-Tom. Fruit tissues were sampled from S. lycopersicum cultivars Micro-Tom, Anthocyanin fruit (Aft, LA1996), Line27859, and Momotaro 8 (Takii, Japan). From Micro-Tom fruit, the peel and the flesh were separately sampled from 4 different ripening stages: mature green (MG, approximately 30 day after anthesis), yellow (Y, approximately 35 days after anthesis), orange (O, approximately 38-40 days after anthesis), and red (R, approximately 45-48 days after anthesis). From fruits of Aft and Line27859, the peel and the flesh were sampled at mature green (MG, approximately 40 days after anthesis) and red (R, approximately 50-55 days after anthesis) stages. From Momotaro 8, the peel and the flesh were sampled at red (R, 50- approximately 50-55 days after anthesis) stages. For each tissue type, 2-4 biological replicates were made in RNA preparation.
Experimental design links: GEO: GSE19326
ArrayExpress:Files: E-GEOD-19326
Publications  
YearTitleSeries
2010Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module.DNA research : an international journal for rapid publication of reports on genes and genomes
Experiments (24)  
ExperimentTargetOntologies
Gene expression data from Aft mature green fruit fleshGSM480200 extract 1
GSM480201 extract 1
GSM480202 extract 1
PO:0007036 (beginning of whole plant fruit ripening stage)
PO:0009086 (endocarp)
PO:0009087 (mesocarp)
SP:0000016 (anthocyanin content)
Gene expression data from Aft mature green fruit peelGSM480206 extract 1
GSM480207 extract 1
GSM480208 extract 1
PO:0007036 (beginning of whole plant fruit ripening stage)
PO:0009085 (exocarp)
SP:0000016 (anthocyanin content)
Gene expression data from Aft red fruit fleshGSM480203 extract 1
GSM480204 extract 1
GSM480205 extract 1
PO:0007050 (late whole plant fruit ripening stage)
PO:0009086 (endocarp)
PO:0009087 (mesocarp)
SP:0000016 (anthocyanin content)
Gene expression data from Aft red fruit peelGSM480209 extract 1
GSM480210 extract 1
GSM480211 extract 1
PO:0007050 (late whole plant fruit ripening stage)
PO:0009085 (exocarp)
SP:0000016 (anthocyanin content)
Gene expression data from Line27859 mature green fruit fleshGSM480212 extract 1
GSM480213 extract 1
GSM480214 extract 1
PO:0007036 (beginning of whole plant fruit ripening stage)
PO:0009086 (endocarp)
PO:0009087 (mesocarp)
Gene expression data from Line27859 mature green fruit peelGSM480218 extract 1
GSM480219 extract 1
GSM480220 extract 1
PO:0007036 (beginning of whole plant fruit ripening stage)
PO:0009085 (exocarp)
Gene expression data from Line27859 red fruit fleshGSM480215 extract 1
GSM480216 extract 1
GSM480217 extract 1
PO:0007050 (late whole plant fruit ripening stage)
PO:0009086 (endocarp)
PO:0009087 (mesocarp)
Gene expression data from Line27859 red fruit peelGSM480221 extract 1
GSM480222 extract 1
GSM480223 extract 1
PO:0007050 (late whole plant fruit ripening stage)
PO:0009085 (exocarp)
Gene expression data from Micro-Tom 3rd leafGSM480172 extract 1
GSM480173 extract 1
PO:0009025 (vascular leaf)
Gene expression data from Micro-Tom cotyledonGSM480170 extract 1
GSM480171 extract 1
PO:0020030 (cotyledon)
Gene expression data from Micro-Tom hypocotylGSM480168 extract 1
GSM480169 extract 1
PO:0020100 (hypocotyl)
Gene expression data from Micro-Tom mature green fruit fleshGSM480180 extract 1
GSM480181 extract 1
GSM480182 extract 1
PO:0007036 (beginning of whole plant fruit ripening stage)
PO:0009086 (endocarp)
PO:0009087 (mesocarp)
Gene expression data from Micro-Tom mature green fruit peelGSM480190 extract 1
GSM480191 extract 1
GSM480192 extract 1
PO:0007036 (beginning of whole plant fruit ripening stage)
PO:0009085 (exocarp)
Gene expression data from Micro-Tom orange fruit fleshGSM480185 extract 1
GSM480186 extract 1
PO:0007031 (mid whole plant fruit ripening stage)
PO:0009086 (endocarp)
PO:0009087 (mesocarp)
Gene expression data from Micro-Tom orange fruit peelGSM480195 extract 1
GSM480196 extract 1
PO:0007031 (mid whole plant fruit ripening stage)
PO:0009085 (exocarp)
Gene expression data from Micro-Tom red fruit fleshGSM480187 extract 1
GSM480188 extract 1
GSM480189 extract 1
PO:0007050 (late whole plant fruit ripening stage)
PO:0009086 (endocarp)
PO:0009087 (mesocarp)
Gene expression data from Micro-Tom red fruit peelGSM480197 extract 1
GSM480198 extract 1
GSM480199 extract 1
PO:0007050 (late whole plant fruit ripening stage)
PO:0009085 (exocarp)
Gene expression data from Micro-Tom rootGSM480165 extract 1
GSM480166 extract 1
GSM480167 extract 1
PO:0009005 (root)
Gene expression data from Micro-Tom yellow fruit fleshGSM480183 extract 1
GSM480184 extract 1
PO:0007001 (early whole plant fruit ripening stage)
PO:0009086 (endocarp)
PO:0009087 (mesocarp)
Gene expression data from Micro-Tom yellow fruit peelGSM480193 extract 1
GSM480194 extract 1
PO:0007001 (early whole plant fruit ripening stage)
PO:0009085 (exocarp)
Gene expression data from Momotaro8 red fruit fleshGSM480224 extract 1
GSM480225 extract 1
GSM480226 extract 1
GSM480227 extract 1
PO:0007050 (late whole plant fruit ripening stage)
PO:0009086 (endocarp)
PO:0009087 (mesocarp)
Gene expression data from Momotaro8 red fruit peelGSM480228 extract 1
GSM480229 extract 1
GSM480230 extract 1
GSM480231 extract 1
PO:0007050 (late whole plant fruit ripening stage)
PO:0009085 (exocarp)
Gene expression data from all leaves of 3-week-old Micro-Tom plantGSM480174 extract 1
GSM480175 extract 1
GSM480176 extract 1
PO:0009025 (vascular leaf)
Gene expression data from all leaves of 5-week-old Micro-Tom plantGSM480177 extract 1
GSM480178 extract 1
GSM480179 extract 1
PO:0009025 (vascular leaf)