Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.3.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04783	0.997
27DAP/17DAP	0.69413	0.149
39DAP/27DAP	0.71873	0.414
41DAP/39DAP	0.93905	0.726
42DAP/41DAP	0.84012	0.774
43DAP/42DAP	0.90971	0.846
47DAP/43DAP	0.95321	0.825
52DAP/47DAP	1.24998	0.605
57DAP/52DAP	1.07955	0.962

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75944	0.025
17DAP/reference	0.61967	0.007
27DAP/reference	0.9856	0.694
39DAP/reference	0.75463	0.009
41DAP/reference	0.63626	0.008
42DAP/reference	1.02754	0.628
43DAP/reference	0.87803	0.073
47DAP/reference	1.0427	1
52DAP/reference	1.55472	0.035
57DAP/reference	1.65569	0.012

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.42022
27DAP/17DAP	0.83492	0.821
39DAP/27DAP	0.70831	0.4
41DAP/39DAP	1.42267	0.817
42DAP/41DAP	0.69044
43DAP/42DAP	0.8865	0.751
47DAP/43DAP	0.75234	0.265
52DAP/47DAP	1.09765	0.962
57DAP/52DAP	0.92214
57DAP/7DAP	1.218	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99416	0.682
17DAP/reference	0.99144	0.599
27DAP/reference	1.18898	0.03
39DAP/reference	1.13776	0.086
41DAP/reference	0.95956	0.326
42DAP/reference	1.03471	0.889
43DAP/reference	1.03224	0.974
47DAP/reference	1.1415	0.377
52DAP/reference	0.96475	0.435
57DAP/reference	1.0496	0.438

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77139	0.064
17DAP/reference	0.7738	0.02
27DAP/reference	1.07508	0.822
39DAP/reference	1.31762	0.255
41DAP/reference	1.48359	0.029
42DAP/reference	1.22215	0.074
43DAP/reference	0.85858	0.201
47DAP/reference	0.89274	0.03
52DAP/reference	1.14016	0.168
57DAP/reference	0.68235	0.021

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89642	0.042
17DAP/reference	0.91654	0.348
27DAP/reference	1.1067	0.198
39DAP/reference	1.12243	0.052
41DAP/reference	1.06128	0.425
42DAP/reference	1.14183	0.416
43DAP/reference	1.12547	0.855
47DAP/reference	0.96323	0.465
52DAP/reference	0.83264	0.132
57DAP/reference	2.24626	0.012

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.52652	0.752
26DAP/20DAP	1.3831
34DAP/26DAP	0.77177	0.741
51DAP/34DAP	0.82884	0.436
52DAP/51DAP	0.61416	1
53DAP/52DAP	1.64261	0.858
55DAP/53DAP	1.14627	0.671
57DAP/55DAP	0.99542	0.867
62DAP/57DAP	1.1443	0.622
68DAP/62DAP	2.59276	0.034
68DAP/14DAP	3.1631	0.021

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.73002	0.322

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.31401	0.059
Mature Green Tomato/Ripe Tomato	2.32031	0.016
Immature Eggplant/Mature Eggplant	0.95539	0.594
Ripe Pepper/Ripe Tomato	0.63547	1
Mature Eggplant/Ripe Tomato	1.95169

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98732
1-1-2/M82	0.88602
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.81855
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.05027	1
4-3/M82	N/A	N/A
5-3/M82	1.20609	0.572
6-2/M82	N/A	N/A
6-3/M82	0.93036
7-1/M82	1.0764	1
7-2/M82	N/A	N/A
9-3-2/M82	1.03266

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.90865	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.03603	1
IL12-4/WTpooled	0.87307	0.581
IL1-4/WTpooled	0.86292
WT/WTpooled	0.98579	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97017	1
DC3000/delta hrp 6h	0.99596	0.95
DC3000/delta hrp 12h	1.02862	1
DC3000/delta hrp 24h	1.23467	0.232

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	1.1557	1
Exp 36h	1.88399	1
Exp 60h	1.81297	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
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	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.92734	0.338
transgenic ySAMdc/azygous control (breaker)	1.08656	1
transgenic ySAMdc/azygous control (red)	0.90168	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08515	0.148

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.41086	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.58844	0.105
Manapal/WT (break)	1.38143	0.183
Manapal/WT (red)	0.74296	0.36