Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.14.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.44556	0.148
27DAP/17DAP	0.53751	0.036
39DAP/27DAP	0.70535	0.325
41DAP/39DAP	1.04674	0.894
42DAP/41DAP	1.00737	1
43DAP/42DAP	1.00651	0.937
47DAP/43DAP	0.8648	0.576
52DAP/47DAP	1.10434	0.906
57DAP/52DAP	1.02145	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.5721	0.025
17DAP/reference	0.46229	0.008
27DAP/reference	0.42177	0.016
39DAP/reference	0.35875	0.015
41DAP/reference	0.34471	0.009
42DAP/reference	0.4035	0.001
43DAP/reference	0.56732	0.056
47DAP/reference	0.36753	0.001
52DAP/reference	0.41075	0.027
57DAP/reference	0.68888	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.64824	0.036
27DAP/17DAP	0.71897	0.363
39DAP/27DAP	0.48747	0.028
41DAP/39DAP	1.10789	0.176
42DAP/41DAP	0.90796	0.135
43DAP/42DAP	0.80553	0.024
47DAP/43DAP	0.93295	0.577
52DAP/47DAP	0.96371	0.839
57DAP/52DAP	0.92607	0.43
57DAP/7DAP	0.67804	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05673	0.813
17DAP/reference	0.81889	0.025
27DAP/reference	0.51775	0.01
39DAP/reference	0.42846	0.011
41DAP/reference	0.37284	0.009
42DAP/reference	0.33677	0.01
43DAP/reference	0.33153	0.011
47DAP/reference	0.29344	0.026
52DAP/reference	0.32571	0.01
57DAP/reference	0.35816	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.47471	0.01
17DAP/reference	0.43458	0.007
27DAP/reference	0.60622	0.041
39DAP/reference	0.31944	0.009
41DAP/reference	0.43293	0.007
42DAP/reference	0.32837	0.011
43DAP/reference	0.36506	0.004
47DAP/reference	0.34194	0.007
52DAP/reference	0.19081	0.003
57DAP/reference	0.13304	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.14227	0.021
17DAP/reference	1.56061	0.269
27DAP/reference	1.50172	0.043
39DAP/reference	1.11226	1
41DAP/reference	0.69789	0.043
42DAP/reference	0.54137	0.019
43DAP/reference	0.5091	0.023
47DAP/reference	0.2378	0.004
52DAP/reference	0.43173	0.058
57DAP/reference	0.78093	0.1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99103	1
26DAP/20DAP	1.16322	0.689
34DAP/26DAP	0.90385	0.575
51DAP/34DAP	0.53116	0.049
52DAP/51DAP	1.07016	0.313
53DAP/52DAP	0.81717	0.245
55DAP/53DAP	1.03046	0.964
57DAP/55DAP	0.92934	0.644
62DAP/57DAP	1.09047	0.833
68DAP/62DAP	0.93382	0.722
68DAP/14DAP	0.42386	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.4628	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.65359	0.058
Mature Green Tomato/Ripe Tomato	4.21044	0.017
Immature Eggplant/Mature Eggplant	0.34988	0.057
Ripe Pepper/Ripe Tomato	7.62099	0.258
Mature Eggplant/Ripe Tomato	34.871	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.95525	0.358
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	1.03634	1
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.99424
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.86129
7-2/M82	N/A	N/A
9-3-2/M82	1.8196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.57065
IL2-6/WTpooled	0.87417	1
IL7-5/WTpooled	1.12118	0.792
IL7-3/WTpooled	0.58308	0.31
IL12-4/WTpooled	1.07994	0.624
IL1-4/WTpooled	0.86345	0.834
WT/WTpooled	1.01051	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	1.12429	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96987	1
DC3000/delta hrp 6h	0.89522	0.95
DC3000/delta hrp 12h	0.64034	1
DC3000/delta hrp 24h	0.91533	0.43

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.85395	0.273
DC3000 delta B/DC3000 delta AB	0.65012	0.093

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06894	1
Exp 36h	0.91962	0.699
Exp 60h	1.00146	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00433	1
Var 0h	1.07142	0.594
Var 12h I row2-row1	1.12243	0.406
Var 12h NI row2-row1	0.98412	0.906
Var 36h I row2-row1	1.16522	1
Var 36h NI row2-row1	1.08524	1
Var 60h I row2-row1	1.24292	0.543
Var 60h NI row2-row1	1.00805	1
Time course 0hI-0hNI	1.05474	0.833
Time course 12hI-12hNI	1.07298	0.572
Time course 36hI-36hNI	1.08848	0.147
Time course 60hI-60hNI	0.96392	0.646

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)	1.09872	0.921
transgenic ySAMdc/azygous control (breaker)	3.60312	0.162
transgenic ySAMdc/azygous control (red)	1.04545	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.40244	0.07

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.40937	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	21.7356	0.083
Manapal/WT (break)	12.7487	0.123
Manapal/WT (red)	3.05504	0.413