Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.4.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99921	0.858
27DAP/17DAP	0.91478	0.817
39DAP/27DAP	0.58953	0.123
41DAP/39DAP	0.93264	0.701
42DAP/41DAP	1.45006	0.441
43DAP/42DAP	1.64994	0.296
47DAP/43DAP	1.21178	0.364
52DAP/47DAP	1.17406	0.95
57DAP/52DAP	1.09081	0.982

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.66781	0.011
17DAP/reference	1.26238	0.22
27DAP/reference	1.38802	0.277
39DAP/reference	0.79055	0.103
41DAP/reference	0.80279	0.201
42DAP/reference	1.08362	0.504
43DAP/reference	0.75734
47DAP/reference	0.75964	0.071
52DAP/reference	0.80183	0.073
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86628	0.245
27DAP/17DAP	1.00101	0.943
39DAP/27DAP	0.95496	0.859
41DAP/39DAP	0.91979	0.764
42DAP/41DAP	1.04149	0.935
43DAP/42DAP	1.14169	0.585
47DAP/43DAP	0.89053	0.559
52DAP/47DAP	1.10117	0.835
57DAP/52DAP	0.97084	0.605
57DAP/7DAP	1.03558	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.86214	0.028
17DAP/reference	1.28573	0.084
27DAP/reference	1.27921	0.088
39DAP/reference	1.7545	0.016
41DAP/reference	1.79832	0.056
42DAP/reference	1.20462	0.076
43DAP/reference	1.07577	0.386
47DAP/reference	0.81057	0.168
52DAP/reference	1.25582	0.021
57DAP/reference	1.07458	0.438

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26522	0.224
17DAP/reference	1.29459	0.12
27DAP/reference	1.32966	0.249
39DAP/reference	0.86955	0.183
41DAP/reference	1.16006	0.831
42DAP/reference	1.19625	0.089
43DAP/reference	0.83699	0.121
47DAP/reference	0.85502	0.029
52DAP/reference	0.86947	0.203
57DAP/reference	0.93518	0.519

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	6.96079	0.015
17DAP/reference	1.46073	0.043
27DAP/reference	2.10632	0.179
39DAP/reference	1.14216	0.254
41DAP/reference	1.17802	0.306
42DAP/reference	5.80041	0.076
43DAP/reference	6.20016	0.011
47DAP/reference	0.72486	0.005
52DAP/reference	6.67166	0.095
57DAP/reference	2.18907	0.233

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.76723	0.89
26DAP/20DAP	1.19877	0.594
34DAP/26DAP	0.64414	0.057
51DAP/34DAP	0.48583
52DAP/51DAP	0.94562	1
53DAP/52DAP	1.18399
55DAP/53DAP	0.80466	0.065
57DAP/55DAP	0.94367	0.76
62DAP/57DAP	0.34984
68DAP/62DAP	0.86816	0.81
68DAP/14DAP	0.46172	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.96464	0.607

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.77491	0.058
Mature Green Tomato/Ripe Tomato	5.05048	0.016
Immature Eggplant/Mature Eggplant	0.19579	0.063
Ripe Pepper/Ripe Tomato	4.89328	0.256
Mature Eggplant/Ripe Tomato	9.05643	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.95602	1
12-2/M82	N/A	N/A
12-4/M82	0.84611	0.282
1-3/M82	1.08847	0.248
2-1-1/M82	0.47184
2-1/M82	N/A	N/A
2-6/M82	1.74297
3-2/M82	1.04935
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.31137
5-3/M82	0.87929	0.419
6-2/M82	0.88428
6-3/M82	0.7844	0.982
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.87449	1
IL2-6/WTpooled	0.93934	1
IL7-5/WTpooled	0.94876	1
IL7-3/WTpooled	1.169
IL12-4/WTpooled	0.95776	1
IL1-4/WTpooled	0.95027	0.834
WT/WTpooled	0.91458	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	0.80609	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94372	1
DC3000/delta hrp 6h	1.0257	1
DC3000/delta hrp 12h	1.18158	1
DC3000/delta hrp 24h	0.48127	0.034

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	0.47857	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.17554	1
Exp 36h	0.65987	0.456
Exp 60h	0.64826	0.266

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98126	1
Var 0h	1.31167	0.98
Var 12h I row2-row1	0.73102	0.338
Var 12h NI row2-row1	0.99427	1
Var 36h I row2-row1	0.78555	0.805
Var 36h NI row2-row1	1.55894	1
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	1.00985	1
Time course 0hI-0hNI	0.86297	0.121
Time course 12hI-12hNI	1.00592	1
Time course 36hI-36hNI	0.85268	0.045
Time course 60hI-60hNI	0.22354	0.006

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)	0.84664	0.428
transgenic ySAMdc/azygous control (breaker)	1.98206	0.178
transgenic ySAMdc/azygous control (red)	1.01146	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.78333	0.043

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.70145	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.94035	0.083
Manapal/WT (break)	1.97225	0.14
Manapal/WT (red)	1.88275	0.133