Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.8.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.77148	0.285
27DAP/17DAP	0.92802	0.73
39DAP/27DAP	1.34453	0.59
41DAP/39DAP	1.01468	0.72
42DAP/41DAP	0.86788	1
43DAP/42DAP	1.15082	0.861
47DAP/43DAP	0.79192	0.386
52DAP/47DAP	1.12956	0.811
57DAP/52DAP	1.10597	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19886	0.025
17DAP/reference	0.82411	0.053
27DAP/reference	0.9436	0.314
39DAP/reference	0.98745	0.762
41DAP/reference	0.98104	0.814
42DAP/reference	1.21027	0.003
43DAP/reference	0.98801	0.785
47DAP/reference	1.65253	0.002
52DAP/reference	1.50446	0.024
57DAP/reference	1.23743	0.024

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.27547	0.179
27DAP/17DAP	1.24075	0.378
39DAP/27DAP	0.99096	0.925
41DAP/39DAP	1.18925	0.968
42DAP/41DAP	1.32724	0.687
43DAP/42DAP	0.85903	0.189
47DAP/43DAP	1.07654	0.865
52DAP/47DAP	1.0928	0.823
57DAP/52DAP	1.17585	0.448
57DAP/7DAP	1.48198	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18311	0.209
17DAP/reference	1.1386	0.244
27DAP/reference	1.13261	0.664
39DAP/reference	0.95531	0.474
41DAP/reference	1.07999	0.864
42DAP/reference	0.85978	0.13
43DAP/reference	0.90125	0.132
47DAP/reference	1.40926	0.017
52DAP/reference	1.23429	0.13
57DAP/reference	1.1279	0.147

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90477	0.306
17DAP/reference	0.78513	0.05
27DAP/reference	1.40361	0.195
39DAP/reference	1.1978	0.571
41DAP/reference	1.08387	0.48
42DAP/reference	1.31448	0.025
43DAP/reference	1.03614	0.892
47DAP/reference	1.32004	0.054
52DAP/reference	0.73255	0.007
57DAP/reference	0.66769	0.009

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02048	1
17DAP/reference	0.85274	0.154
27DAP/reference	1.13815	0.125
39DAP/reference	1.26032	0.245
41DAP/reference	1.37545	0.181
42DAP/reference	1.29434	0.209
43DAP/reference	1.40288	0.096
47DAP/reference	0.93285	0.325
52DAP/reference	1.28443	0.167
57DAP/reference	2.28762	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.13175	0.966
26DAP/20DAP	1.73063	0.249
34DAP/26DAP	0.77907	0.412
51DAP/34DAP	3.30808	0.031
52DAP/51DAP	0.83892	1
53DAP/52DAP	1.52278	0.086
55DAP/53DAP	0.67219	0.028
57DAP/55DAP	0.75372	0.149
62DAP/57DAP	0.47986	0.01
68DAP/62DAP	1.34838	0.1
68DAP/14DAP	2.3941	0.016

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.52759	0.038

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.77986	0.236
Mature Green Tomato/Ripe Tomato	1.28674	0.237
Immature Eggplant/Mature Eggplant	1.56932	0.067
Ripe Pepper/Ripe Tomato	1.08753	1
Mature Eggplant/Ripe Tomato	0.76161	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.5398
1-1-2/M82	1.05394	1
12-2/M82	0.946
12-4/M82	0.8462	1
1-3/M82	2.54322
2-1-1/M82	1.07407
2-1/M82	N/A	N/A
2-6/M82	0.71802	0.501
3-2/M82	1.10619	1
4-1-1/M82	0.70734	1
4-1/M82	0.69196
4-3-2/M82	0.80926	0.445
4-3/M82	1.27514	1
5-3/M82	1.29615	0.572
6-2/M82	N/A	N/A
6-3/M82	0.78948
7-1/M82	N/A	N/A
7-2/M82	1.11042
9-3-2/M82	0.95549	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.96499
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.10305
IL12-4/WTpooled	0.90485
IL1-4/WTpooled	1.09641	1
WT/WTpooled	0.95898	1

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	1.0942	0.853

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04293	0.921
DC3000/delta hrp 6h	0.9986	0.95
DC3000/delta hrp 12h	0.96141	1
DC3000/delta hrp 24h	0.83498	0.202

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.26551	0.053
DC3000 delta B/DC3000 delta AB	1.5422	0.115

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.1874	1
Exp 36h	1.36608	0.693
Exp 60h	1.54535	0.283

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	1.02672	1
Var 0h	0.54695	0.936
Var 12h I row2-row1	1.10606	0.654
Var 12h NI row2-row1	1.10807	0.649
Var 36h I row2-row1	1.05843	1
Var 36h NI row2-row1	0.94632	0.706
Var 60h I row2-row1	0.60924	0.285
Var 60h NI row2-row1	1.04783	1
Time course 0hI-0hNI	1.03181	0.867
Time course 12hI-12hNI	1.13936	0.26
Time course 36hI-36hNI	1.37504	0.006
Time course 60hI-60hNI	3.36919	0.008

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	0.8511	0.362
transgenic ySAMdc/azygous control (breaker)	0.67262	0.251
transgenic ySAMdc/azygous control (red)	1.02123	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.12693	0.119

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.73353	0.238

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.94531	1
Manapal/WT (break)	1.45758	0.183
Manapal/WT (red)	0.87549	0.181