Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.19.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.30693	0.485
27DAP/17DAP	1.4733	0.521
39DAP/27DAP	1.7523	0.057
41DAP/39DAP	1.0422	0.982
42DAP/41DAP	1.57474	0.199
43DAP/42DAP	1.46725	0.993
47DAP/43DAP	3.37709	0.187
52DAP/47DAP	0.46158	0.052
57DAP/52DAP	1.29985	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.46554	0.147
17DAP/reference	2.04564	0.528
27DAP/reference	1.91568	0.058
39DAP/reference	0.98763	0.885
41DAP/reference	1.33753	0.122
42DAP/reference	1.36952	0.093
43DAP/reference	1.50815	0.014
47DAP/reference	1.39248	0.254
52DAP/reference	2.04459	0.008
57DAP/reference	2.07874	0.041

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19137	0.247
27DAP/17DAP	1.00882	1
39DAP/27DAP	1.16857	0.259
41DAP/39DAP	0.73409	0.059
42DAP/41DAP	1.23695	0.225
43DAP/42DAP	1.14262	0.23
47DAP/43DAP	1.085	0.389
52DAP/47DAP	1.27026	0.338
57DAP/52DAP	1.18775	0.272
57DAP/7DAP	1.54668	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74252	0.08
17DAP/reference	0.7951	0.044
27DAP/reference	0.86027	0.016
39DAP/reference	1.02856	1
41DAP/reference	0.8821	0.098
42DAP/reference	0.98267	0.582
43DAP/reference	0.79651	0.025
47DAP/reference	0.83049	0.066
52DAP/reference	0.87148	0.097
57DAP/reference	0.87244	0.123

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18871
17DAP/reference	1.05714	0.873
27DAP/reference	1.4288	0.02
39DAP/reference	1.50696	0.024
41DAP/reference	1.34772	0.106
42DAP/reference	1.27478	0.259
43DAP/reference	0.91166	0.43
47DAP/reference	1.23499	0.282
52DAP/reference	1.32584
57DAP/reference	N/A	N/A

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77548	0.082
17DAP/reference	0.92645	0.47
27DAP/reference	0.71251	0.025
39DAP/reference	0.71628	0.023
41DAP/reference	0.83893	0.119
42DAP/reference	1.08461	1
43DAP/reference	1.14731	0.572
47DAP/reference	N/A	N/A
52DAP/reference	0.90012	0.464
57DAP/reference	2.05884	0.044

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.20457	0.966
26DAP/20DAP	1.06697	1
34DAP/26DAP	1.42256	1
51DAP/34DAP	0.63904	0.292
52DAP/51DAP	2.40029	0.049
53DAP/52DAP	0.71226	0.05
55DAP/53DAP	1.43103	0.039
57DAP/55DAP	0.46192	0.026
62DAP/57DAP	1.18596	0.935
68DAP/62DAP	0.97398	0.885
68DAP/14DAP	1.43926	0.04

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.79301	0.054

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.56862	0.045
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.54025	0.224
Mature Eggplant/Ripe Tomato	0.64405

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98106	0.961
1-1-2/M82	0.90463	1
12-2/M82	N/A	N/A
12-4/M82	1.33111	1
1-3/M82	0.72556	0.339
2-1-1/M82	0.74466	0.92
2-1/M82	N/A	N/A
2-6/M82	1.0243	0.695
3-2/M82	1.0254	1
4-1-1/M82	0.9316	1
4-1/M82	0.89897	1
4-3-2/M82	1.55165	0.241
4-3/M82	0.90872	0.72
5-3/M82	0.95292	1
6-2/M82	0.66511	0.481
6-3/M82	0.94253
7-1/M82	1.19081
7-2/M82	1.01375	1
9-3-2/M82	1.32158

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.16815	0.493
IL2-6/WTpooled	1.01668	1
IL7-5/WTpooled	0.53335
IL7-3/WTpooled	1.19578	1
IL12-4/WTpooled	1.22632	0.516
IL1-4/WTpooled	1.00727	1
WT/WTpooled	1.01666	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	1.16607	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06264	0.921
DC3000/delta hrp 6h	0.92248
DC3000/delta hrp 12h	0.80702	1
DC3000/delta hrp 24h	1.05189	0.582

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.05755	0.27
DC3000 delta B/DC3000 delta AB	1.23711	0.24

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	0.96794	1
Var 0h	0.56432	0.98
Var 12h I row2-row1	0.94667	0.77
Var 12h NI row2-row1	1.00642	1
Var 36h I row2-row1	1.07933	1
Var 36h NI row2-row1	1.28933	0.276
Var 60h I row2-row1	0.95186	0.952
Var 60h NI row2-row1	1.07473	1
Time course 0hI-0hNI	1.02524	0.833
Time course 12hI-12hNI	0.94232	0.546
Time course 36hI-36hNI	0.91175	0.144
Time course 60hI-60hNI	0.67753	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)	0.80302	0.529
transgenic ySAMdc/azygous control (breaker)	1.33709	1
transgenic ySAMdc/azygous control (red)	0.91148	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.81719	0.049

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.22222	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.2883	1
Manapal/WT (break)	0.91774	1
Manapal/WT (red)	1.12041	0.142