Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.16.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.76541	0.101
27DAP/17DAP	0.88792	0.724
39DAP/27DAP	1.12459	0.83
41DAP/39DAP	0.63183	0.06
42DAP/41DAP	0.7635	0.397
43DAP/42DAP	1.20837	0.772
47DAP/43DAP	0.60987	0.077
52DAP/47DAP	1.07527	0.918
57DAP/52DAP	1.08652	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8715	0.145
17DAP/reference	0.69867	0.009
27DAP/reference	0.86353	0.152
39DAP/reference	0.74306	0.018
41DAP/reference	0.56767	0.008
42DAP/reference	0.90853	0.111
43DAP/reference	0.86484	0.034
47DAP/reference	0.97633	0.473
52DAP/reference	1.086	0.607
57DAP/reference	1.19435	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91211	0.17
27DAP/17DAP	1.07021	0.754
39DAP/27DAP	0.80083	0.083
41DAP/39DAP	1.09655	0.88
42DAP/41DAP	0.9719	0.737
43DAP/42DAP	0.95346	0.597
47DAP/43DAP	0.98386	0.923
52DAP/47DAP	0.75716	0.069
57DAP/52DAP	0.95883	0.7
57DAP/7DAP	0.46758	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.10127	0.027
17DAP/reference	2.90829	0.006
27DAP/reference	2.54944	0.006
39DAP/reference	2.31638	0.005
41DAP/reference	2.5485	0.01
42DAP/reference	2.99356	0.006
43DAP/reference	3.72126	0.007
47DAP/reference	2.25193	0.182
52DAP/reference	2.90937	0.007
57DAP/reference	2.83067	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.69921	0.023
17DAP/reference	0.63676	0.004
27DAP/reference	0.96931	0.501
39DAP/reference	1.01168	0.702
41DAP/reference	1.144	0.146
42DAP/reference	1.04712	0.68
43DAP/reference	0.57707	0.014
47DAP/reference	0.80924	0.017
52DAP/reference	0.88176	0.066
57DAP/reference	0.62416	0.02

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.35333	0.023
17DAP/reference	1.37944	0.689
27DAP/reference	2.87513	0.021
39DAP/reference	3.01779	0.01
41DAP/reference	2.33699	0.01
42DAP/reference	3.00456	0.007
43DAP/reference	2.51145	0.011
47DAP/reference	0.9748	0.478
52DAP/reference	3.06808	0.225
57DAP/reference	2.82652	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08266	0.966
26DAP/20DAP	2.18307	0.138
34DAP/26DAP	0.95824	0.917
51DAP/34DAP	1.12341	0.271
52DAP/51DAP	1.05798	0.808
53DAP/52DAP	1.06226	0.83
55DAP/53DAP	0.71129	0.045
57DAP/55DAP	0.9562	0.736
62DAP/57DAP	1.24122	0.217
68DAP/62DAP	3.26128	0.071
68DAP/14DAP	4.03994	0.029

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.01131	0.016

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.02286	0.666
Mature Green Tomato/Ripe Tomato	1.92714	0.237
Immature Eggplant/Mature Eggplant	0.93867	0.159
Ripe Pepper/Ripe Tomato	0.63427	0.224
Mature Eggplant/Ripe Tomato	1.08992	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.94425	0.944
1-1-2/M82	1.05645	1
12-2/M82	0.94852
12-4/M82	1.11391	1
1-3/M82	1.04605	0.479
2-1-1/M82	0.90714	1
2-1/M82	0.95981	1
2-6/M82	0.91843	1
3-2/M82	1.45456
4-1-1/M82	1.16641
4-1/M82	N/A	N/A
4-3-2/M82	0.81336
4-3/M82	1.06138	1
5-3/M82	1.08131	1
6-2/M82	N/A	N/A
6-3/M82	1.07197	1
7-1/M82	1.10991	0.992
7-2/M82	0.87905	0.796
9-3-2/M82	1.44269

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	1.05042	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98351	1
DC3000/delta hrp 6h	1.0251	1
DC3000/delta hrp 12h	0.98317	1
DC3000/delta hrp 24h	1.02253	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.2626	0.042
DC3000 delta B/DC3000 delta AB	1.4234	0.093

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06973	0.254
Exp 36h	1.43139	0.409
Exp 60h	1.31628	0.215

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00308	1
Var 0h	1.46171	0.936
Var 12h I row2-row1	0.85548	0.338
Var 12h NI row2-row1	1.11923	0.281
Var 36h I row2-row1	1.24003	0.41
Var 36h NI row2-row1	0.86094	0.584
Var 60h I row2-row1	0.85726	0.439
Var 60h NI row2-row1	0.79969	0.756
Time course 0hI-0hNI	1.1206	0.603
Time course 12hI-12hNI	0.99089	0.984
Time course 36hI-36hNI	1.45029	0.01
Time course 60hI-60hNI	1.8482	0.008

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)	1.08339	0.268
transgenic ySAMdc/azygous control (breaker)	1.06467	1
transgenic ySAMdc/azygous control (red)	0.97867	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04866	0.35

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.07764	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.1292	1
Manapal/WT (break)	1.10756	0.381
Manapal/WT (red)	1.08754	1