Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.19.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94316	0.664
27DAP/17DAP	1.16273	0.844
39DAP/27DAP	1.00162	0.782
41DAP/39DAP	0.96645	0.857
42DAP/41DAP	0.76268	0.774
43DAP/42DAP	0.84296	0.705
47DAP/43DAP	0.99357	0.904
52DAP/47DAP	1.46876	0.403
57DAP/52DAP	1.29764	0.787

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.46889	0.101
17DAP/reference	0.68511	0.021
27DAP/reference	1.22485	0.071
39DAP/reference	0.95249	0.624
41DAP/reference	0.78999	0.085
42DAP/reference	1.07652	0.812
43DAP/reference	0.76713	0.019
47DAP/reference	0.92069	0.148
52DAP/reference	1.20669	0.053
57DAP/reference	0.966	0.456

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99939	0.847
27DAP/17DAP	1.19228	0.69
39DAP/27DAP	0.73804	0.046
41DAP/39DAP	1.27968	0.565
42DAP/41DAP	0.85509	0.412
43DAP/42DAP	1.01098	1
47DAP/43DAP	1.18189	0.827
52DAP/47DAP	0.97692	0.807
57DAP/52DAP	1.49004	0.486
57DAP/7DAP	0.90172	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9688	0.495
17DAP/reference	0.89468	0.124
27DAP/reference	1.0348	0.804
39DAP/reference	0.73664	0.064
41DAP/reference	0.81171	0.166
42DAP/reference	0.76021	0.032
43DAP/reference	0.99428	0.608
47DAP/reference	1.0538	1
52DAP/reference	0.76408	0.018
57DAP/reference	0.93539	0.24

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2121	0.093
17DAP/reference	0.85127	0.099
27DAP/reference	1.17973	0.297
39DAP/reference	1.17975	0.272
41DAP/reference	1.03946	1
42DAP/reference	0.9539	0.355
43DAP/reference	0.8252	0.035
47DAP/reference	0.86023	0.049
52DAP/reference	0.94179	0.351
57DAP/reference	0.82642	0.085

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95619	0.422
17DAP/reference	0.90308	0.308
27DAP/reference	1.15242	0.164
39DAP/reference	0.97848	0.464
41DAP/reference	0.97787	0.512
42DAP/reference	1.09033	0.51
43DAP/reference	1.21355	0.123
47DAP/reference	0.75516	0.041
52DAP/reference	1.47322	0.284
57DAP/reference	1.16686	0.18

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04793	1
26DAP/20DAP	0.98426	1
34DAP/26DAP	1.21905	1
51DAP/34DAP	1.16845	0.207
52DAP/51DAP	1.22751	0.783
53DAP/52DAP	1.2458	0.643
55DAP/53DAP	0.84897	0.619
57DAP/55DAP	1.20304	0.854
62DAP/57DAP	1.04358	0.994
68DAP/62DAP	1.30866	0.573
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.14914	0.821

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.06492	0.666
Mature Green Tomato/Ripe Tomato	0.88871	0.446
Immature Eggplant/Mature Eggplant	1.25967	0.259
Ripe Pepper/Ripe Tomato	0.60156	0.224
Mature Eggplant/Ripe Tomato	0.51592	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.8141
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.96716	1
1-3/M82	1.22055
2-1-1/M82	0.80208	0.465
2-1/M82	N/A	N/A
2-6/M82	1.02106
3-2/M82	N/A	N/A
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	0.90959	0.72
5-3/M82	1.06196	1
6-2/M82	N/A	N/A
6-3/M82	0.78287
7-1/M82	2.2797
7-2/M82	1.72922	1
9-3-2/M82	N/A	N/A

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	0.40761
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.0521
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	1.30899	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97942	1
DC3000/delta hrp 6h	0.82581	0.95
DC3000/delta hrp 12h	0.82412	1
DC3000/delta hrp 24h	1.28606	0.123

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.94915	0.879
Exp 60h	1.26903	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0433	1
Var 0h	0.6761	1
Var 12h I row2-row1	2.45476	0.654
Var 12h NI row2-row1	1.64307	0.649
Var 36h I row2-row1	1.17755	0.291
Var 36h NI row2-row1	0.57188	0.61
Var 60h I row2-row1	0.81707	0.832
Var 60h NI row2-row1	0.69708	0.483
Time course 0hI-0hNI	0.91036	0.852
Time course 12hI-12hNI	1.77522	0.452
Time course 36hI-36hNI	1.48033	0.016
Time course 60hI-60hNI	2.50389	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)	1.08901	0.318
transgenic ySAMdc/azygous control (breaker)	1.08599	0.248
transgenic ySAMdc/azygous control (red)	0.92884	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.11378	0.1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.7257	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.81368	1
Manapal/WT (break)	0.87499	1
Manapal/WT (red)	0.93319	0.424