Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.13.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.464	0.403
27DAP/17DAP	0.65429	0.162
39DAP/27DAP	0.81843	0.462
41DAP/39DAP	1.18302	0.522
42DAP/41DAP	0.87534	0.774
43DAP/42DAP	1.04398	1
47DAP/43DAP	2.08436	0.223
52DAP/47DAP	1.34349	0.562
57DAP/52DAP	1.002	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17457	0.089
17DAP/reference	1.26442	0.1
27DAP/reference	1.03123	0.831
39DAP/reference	1.0863	0.514
41DAP/reference	1.08338	0.393
42DAP/reference	0.83415	0.012
43DAP/reference	1.05194	0.403
47DAP/reference	1.18607	0.044
52DAP/reference	1.4638	0.036
57DAP/reference	1.0954	0.132

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98424	0.763
27DAP/17DAP	1.14443	0.511
39DAP/27DAP	0.84894	0.121
41DAP/39DAP	1.19504	0.801
42DAP/41DAP	0.99326	0.823
43DAP/42DAP	0.88787	0.048
47DAP/43DAP	1.02338	1
52DAP/47DAP	1.79092	0.252
57DAP/52DAP	1.21577	0.806
57DAP/7DAP	1.13967	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12908	0.252
17DAP/reference	1.09967	0.437
27DAP/reference	1.04778	1
39DAP/reference	1.04329	1
41DAP/reference	1.20296	0.035
42DAP/reference	1.0395	0.889
43DAP/reference	0.84322	0.066
47DAP/reference	0.85628	0.168
52DAP/reference	1.01829	1
57DAP/reference	1.1263	0.137

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08484	0.589
17DAP/reference	0.97855	0.611
27DAP/reference	0.87987	0.16
39DAP/reference	0.96623	0.428
41DAP/reference	0.84556	0.08
42DAP/reference	0.93551	0.321
43DAP/reference	1.13225	0.242
47DAP/reference	0.87984	0.149
52DAP/reference	0.93055	0.28
57DAP/reference	0.98021	0.649

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00303	0.75
17DAP/reference	0.87672	0.335
27DAP/reference	1.05641	0.552
39DAP/reference	0.94831	0.43
41DAP/reference	1.05715	0.674
42DAP/reference	1.04524	0.802
43DAP/reference	0.90901	0.305
47DAP/reference	0.84196	0.018
52DAP/reference	0.90462	0.482
57DAP/reference	1.07797	0.436

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.90049	1
26DAP/20DAP	N/A	N/A
34DAP/26DAP	0.60826
51DAP/34DAP	1.2162	0.829
52DAP/51DAP	1.62896
53DAP/52DAP	1.14879	0.99
55DAP/53DAP	1.05128	0.894
57DAP/55DAP	1.10725
62DAP/57DAP	0.79091	0.681
68DAP/62DAP	N/A	N/A
68DAP/14DAP	2.67614	0.328

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.91207	0.466

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.43733	0.018
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.07528	0.224
Mature Eggplant/Ripe Tomato	0.05434	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.10017	0.591
1-1-2/M82	0.91029	1
12-2/M82	1.1373	1
12-4/M82	0.65176
1-3/M82	1.39345
2-1-1/M82	1.15257	0.26
2-1/M82	N/A	N/A
2-6/M82	1.18899
3-2/M82	0.76431
4-1-1/M82	1.46449	1
4-1/M82	N/A	N/A
4-3-2/M82	1.56566	0.508
4-3/M82	0.95431	1
5-3/M82	0.67774	0.395
6-2/M82	0.30834
6-3/M82	1.19318	1
7-1/M82	1.00284
7-2/M82	0.70631	0.527
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.02514	1
IL7-5/WTpooled	0.98756
IL7-3/WTpooled	0.97398	1
IL12-4/WTpooled	1.01305	0.839
IL1-4/WTpooled	0.95305	0.834
WT/WTpooled	0.98738	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	0.68127	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00264	1
DC3000/delta hrp 6h	1.03179	1
DC3000/delta hrp 12h	0.93505	1
DC3000/delta hrp 24h	1.05533	0.655

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01687	1
Var 0h	0.57803	1
Var 12h I row2-row1	1.03648
Var 12h NI row2-row1	0.93761	0.906
Var 36h I row2-row1	1.00675	1
Var 36h NI row2-row1	0.86763	0.61
Var 60h I row2-row1	1.36024
Var 60h NI row2-row1	1.06138	0.904
Time course 0hI-0hNI	0.98476	0.936
Time course 12hI-12hNI	0.89591	0.519
Time course 36hI-36hNI	0.75396	0.093
Time course 60hI-60hNI	0.599	0.015

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)	1.36838	0.213
transgenic ySAMdc/azygous control (breaker)	1.05373	1
transgenic ySAMdc/azygous control (red)	1.03334	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94956	0.071

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.90593	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.18532	0.307
Manapal/WT (break)	2.55453	0.14
Manapal/WT (red)	3.79247	0.134