Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.4.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.45045	0.037
27DAP/17DAP	1.5601	0.73
39DAP/27DAP	1.68926	0.056
41DAP/39DAP	0.58547	0.047
42DAP/41DAP	0.90418	1
43DAP/42DAP	1.46088	0.823
47DAP/43DAP	1.39901	0.52
52DAP/47DAP	1.17244	0.76
57DAP/52DAP	1.81801	0.656

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90403	0.344
17DAP/reference	0.77682	0.224
27DAP/reference	1.24944	0.008
39DAP/reference	1.26618	0.016
41DAP/reference	1.19444	0.013
42DAP/reference	1.56379	0.174
43DAP/reference	1.37224
47DAP/reference	2.07247	0.023
52DAP/reference	1.84662	0.008
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.61949	0.036
27DAP/17DAP	1.28394	0.116
39DAP/27DAP	0.85468	0.311
41DAP/39DAP	1.45595	0.887
42DAP/41DAP	1.05356	0.935
43DAP/42DAP	0.90367	0.293
47DAP/43DAP	0.94852	0.647
52DAP/47DAP	1.30861	0.343
57DAP/52DAP	1.44058	0.054
57DAP/7DAP	2.25141	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03121	1
17DAP/reference	1.39017	0.006
27DAP/reference	1.85745	0.006
39DAP/reference	2.41953	0.005
41DAP/reference	1.57285	0.008
42DAP/reference	1.79146	0.007
43DAP/reference	1.76261	0.006
47DAP/reference	2.3203	0.014
52DAP/reference	2.02787	0.008
57DAP/reference	2.11735	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.56855	0.008
17DAP/reference	1.18531	0.448
27DAP/reference	1.82346	0.013
39DAP/reference	2.03299	0.011
41DAP/reference	1.22521	0.183
42DAP/reference	1.87986	0.066
43DAP/reference	1.09872	0.865
47DAP/reference	2.06696	0.008
52DAP/reference	1.62003	0.006
57DAP/reference	1.09718	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92307	0.362
17DAP/reference	0.78974	0.167
27DAP/reference	1.65652	0.014
39DAP/reference	1.65198	0.004
41DAP/reference	1.47189	0.007
42DAP/reference	2.47636	0.007
43DAP/reference	2.11343	0.006
47DAP/reference	2.16276	0.01
52DAP/reference	2.23247	0.027
57DAP/reference	4.57701	0.005

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09956	0.966
26DAP/20DAP	1.37548	0.147
34DAP/26DAP	1.09642	0.819
51DAP/34DAP	2.07137	0.029
52DAP/51DAP	0.62586	0.151
53DAP/52DAP	1.1295	0.444
55DAP/53DAP	0.7933	0.032
57DAP/55DAP	0.96446	0.821
62DAP/57DAP	0.67361	0.088
68DAP/62DAP	1.0627	0.872
68DAP/14DAP	1.87703	0.021

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.44904	0.045

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.67951	0.179
Mature Green Tomato/Ripe Tomato	1.00392	0.835
Immature Eggplant/Mature Eggplant	0.9314	0.448
Ripe Pepper/Ripe Tomato	0.80624	1
Mature Eggplant/Ripe Tomato	0.41337	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.73833	0.503
1-1-2/M82	1.13447	1
12-2/M82	1.03075	1
12-4/M82	1.03649	1
1-3/M82	1.78105	0.255
2-1-1/M82	1.19422	0.689
2-1/M82	1.01206	1
2-6/M82	1.01714	1
3-2/M82	1.089	0.967
4-1-1/M82	1.00746	1
4-1/M82	1.5128	1
4-3-2/M82	0.76009	0.698
4-3/M82	0.74161	0.441
5-3/M82	1.14139	1
6-2/M82	1.25463	1
6-3/M82	0.93847	1
7-1/M82	1.03588	1
7-2/M82	1.01523	1
9-3-2/M82	0.9804	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.82044
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.97462
IL12-4/WTpooled	0.81224	0.71
IL1-4/WTpooled	1.00334
WT/WTpooled	1.07185	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	1.0519	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09981	0.894
DC3000/delta hrp 6h	1.04094	1
DC3000/delta hrp 12h	1.00585	1
DC3000/delta hrp 24h	1.16133	0.049

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.96267	0.92
DC3000 delta B/DC3000 delta AB	0.95323	0.418

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04713	1
Exp 36h	0.79098	0.539
Exp 60h	0.92536	0.754

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	0.96774	1
Var 12h I row2-row1	0.41092
Var 12h NI row2-row1	0.66241
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)	1.00517	0.921
transgenic ySAMdc/azygous control (breaker)	0.94718	0.49
transgenic ySAMdc/azygous control (red)	0.8831	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.78735	0.042

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88959	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.40168	0.172
Manapal/WT (break)	0.79916	0.333
Manapal/WT (red)	0.6049	0.183