Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.4.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.34824	0.219
27DAP/17DAP	1.26783	0.833
39DAP/27DAP	0.95882	0.682
41DAP/39DAP	0.9282	0.69
42DAP/41DAP	0.78439	0.774
43DAP/42DAP	1.26705	0.553
47DAP/43DAP	1.21535	0.293
52DAP/47DAP	1.14179	0.809
57DAP/52DAP	1.0484	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98345	0.63
17DAP/reference	1.10514	0.035
27DAP/reference	0.98531	0.694
39DAP/reference	1.08479	0.249
41DAP/reference	0.92543	0.667
42DAP/reference	1.05021	0.585
43DAP/reference	0.9151	0.631
47DAP/reference	1.26524	0.017
52DAP/reference	1.00368	0.546
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.49801	0.213
27DAP/17DAP	0.9228	0.821
39DAP/27DAP	0.96469	0.795
41DAP/39DAP	1.11565	0.876
42DAP/41DAP	1.13316	0.571
43DAP/42DAP	1.03079	1
47DAP/43DAP	0.93014	0.637
52DAP/47DAP	1.20528	0.484
57DAP/52DAP	1.07909	0.714
57DAP/7DAP	1.04902	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18828	0.121
17DAP/reference	1.23593	0.18
27DAP/reference	1.20046	0.453
39DAP/reference	1.45008	0.014
41DAP/reference	1.29639	0.048
42DAP/reference	1.40526	0.037
43DAP/reference	1.19906	0.099
47DAP/reference	1.4162	0.03
52DAP/reference	1.56117	0.007
57DAP/reference	1.22908	0.1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9509	0.457
17DAP/reference	0.8876	0.326
27DAP/reference	0.97131	0.537
39DAP/reference	0.95784	0.274
41DAP/reference	1.15688	0.394
42DAP/reference	0.97863	0.482
43DAP/reference	0.87495	0.162
47DAP/reference	1.03716	0.751
52DAP/reference	1.06513	1
57DAP/reference	0.85971	0.092

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.42247	0.018
17DAP/reference	1.13379	0.283
27DAP/reference	0.84799	0.184
39DAP/reference	1.16398	0.235
41DAP/reference	1.45716	0.012
42DAP/reference	2.32334	0.026
43DAP/reference	2.0743	0.069
47DAP/reference	1.14091	0.279
52DAP/reference	2.02221	0.045
57DAP/reference	1.55629	0.03

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10263	0.966
26DAP/20DAP	1.79257	0.574
34DAP/26DAP	0.87965	0.763
51DAP/34DAP	2.11162	0.032
52DAP/51DAP	1.01016	0.954
53DAP/52DAP	1.20203	0.384
55DAP/53DAP	0.6028	0.019
57DAP/55DAP	1.20154	0.666
62DAP/57DAP	0.83119	0.681
68DAP/62DAP	1.20844	0.707
68DAP/14DAP	2.19138	0.023

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.5231	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.50129	0.094
Mature Green Tomato/Ripe Tomato	1.14246	0.814
Immature Eggplant/Mature Eggplant	1.25762	0.058
Ripe Pepper/Ripe Tomato	0.93932	1
Mature Eggplant/Ripe Tomato	0.54071	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.08173	1
1-1-2/M82	1.13498	1
12-2/M82	0.85891	0.74
12-4/M82	1.03015	1
1-3/M82	1.90489	0.248
2-1-1/M82	1.15626
2-1/M82	1.05592	1
2-6/M82	0.95392	1
3-2/M82	1.21048	0.717
4-1-1/M82	0.61921	0.959
4-1/M82	0.65273
4-3-2/M82	1.15521	0.262
4-3/M82	1.40775	1
5-3/M82	1.0817	1
6-2/M82	1.69996	0.235
6-3/M82	N/A	N/A
7-1/M82	1.32445	0.598
7-2/M82	1.08217	1
9-3-2/M82	1.30686	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.01227	1
IL2-6/WTpooled	1.18675	0.46
IL7-5/WTpooled	1.21078	1
IL7-3/WTpooled	0.78035	0.298
IL12-4/WTpooled	1.15111	0.695
IL1-4/WTpooled	1.32971	0.426
WT/WTpooled	0.94799	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	1.03212	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03083	1
DC3000/delta hrp 6h	0.90273	0.95
DC3000/delta hrp 12h	0.94588	1
DC3000/delta hrp 24h	0.92439	0.503

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.0242	0.515
DC3000 delta B/DC3000 delta AB	0.98846	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.80934	1
Exp 36h	1.05397	1
Exp 60h	1.18048	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05212
Var 0h	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	0.86743
Var 36h I row2-row1	0.97213	1
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	1.47837	0.486
Time course 12hI-12hNI	1.10248	0.507
Time course 36hI-36hNI	1.28486	0.007
Time course 60hI-60hNI	1.83419	0.022

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)	0.97401	0.614
transgenic ySAMdc/azygous control (breaker)	0.82994	0.49
transgenic ySAMdc/azygous control (red)	1.22017	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.23117	0.119

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.40197	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.33621	0.14
Manapal/WT (break)	1.13381	0.381
Manapal/WT (red)	1.27781	0.164