Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.11.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88822	0.475
27DAP/17DAP	1.19173	0.845
39DAP/27DAP	0.87189	0.631
41DAP/39DAP	0.71472	0.202
42DAP/41DAP	1.14455	0.882
43DAP/42DAP	0.73846	0.681
47DAP/43DAP	1.16729	0.538
52DAP/47DAP	0.85082	0.521
57DAP/52DAP	0.92796	0.895

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85072	0.217
17DAP/reference	1.36398	0.011
27DAP/reference	1.07374	0.559
39DAP/reference	1.11235	0.335
41DAP/reference	1.14069	0.421
42DAP/reference	0.91513	0.124
43DAP/reference	1.1195	0.269
47DAP/reference	0.90399	0.137
52DAP/reference	0.8967	0.189
57DAP/reference	0.82291	0.042

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08758	0.961
27DAP/17DAP	1.0632	0.954
39DAP/27DAP	0.90422	0.556
41DAP/39DAP	1.4811	0.887
42DAP/41DAP	0.96436	0.762
43DAP/42DAP	1.04136	1
47DAP/43DAP	0.91392	0.63
52DAP/47DAP	0.99522	0.93
57DAP/52DAP	0.98167	0.798
57DAP/7DAP	0.88855

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96372	0.495
17DAP/reference	0.90135	0.253
27DAP/reference	1.017	0.974
39DAP/reference	0.72311	0.043
41DAP/reference	0.84034	0.146
42DAP/reference	0.82787	0.038
43DAP/reference	1.01607	1
47DAP/reference	0.88022	0.293
52DAP/reference	0.94862	0.398
57DAP/reference	0.92529	0.28

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17386	0.077
17DAP/reference	1.15798	0.216
27DAP/reference	0.96627	0.452
39DAP/reference	0.73581	0.016
41DAP/reference	1.05537	1
42DAP/reference	0.78132	0.013
43DAP/reference	1.12257	0.713
47DAP/reference	0.90553	0.214
52DAP/reference	1.04441	0.322
57DAP/reference	1.51793	0.012

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10719	0.207
17DAP/reference	0.9697	0.647
27DAP/reference	1.11047	0.179
39DAP/reference	1.15385	0.112
41DAP/reference	1.15647	0.276
42DAP/reference	0.82962	0.361
43DAP/reference	0.7676	0.131
47DAP/reference	0.89173	0.24
52DAP/reference	0.85074	0.216
57DAP/reference	0.6991	0.034

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10097	0.966
26DAP/20DAP	1.42638	0.312
34DAP/26DAP	1.33428	1
51DAP/34DAP	1.26289	0.746
52DAP/51DAP	0.83559	1
53DAP/52DAP	1.08357	1
55DAP/53DAP	1.23313	0.842
57DAP/55DAP	1.08591	0.904
62DAP/57DAP	3.72164	0.622
68DAP/62DAP	0.72794	0.579
68DAP/14DAP	0.97338	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.28663	0.558

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	1.23685

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.71069
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	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	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	N/A	N/A
7-2/M82	0.75222
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.84536	1
IL2-6/WTpooled	0.9863	1
IL7-5/WTpooled	1.18281	1
IL7-3/WTpooled	1.06787	1
IL12-4/WTpooled	0.79686	0.484
IL1-4/WTpooled	1.05516	1
WT/WTpooled	0.93604	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	0.83395

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.89005	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	1.2917	0.063

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	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	1.12371
Var 0h	0.94612	1
Var 12h I row2-row1	3.55036	0.544
Var 12h NI row2-row1	0.9114
Var 36h I row2-row1	0.84551	1
Var 36h NI row2-row1	0.70896	0.482
Var 60h I row2-row1	1.11392	1
Var 60h NI row2-row1	0.64072	1
Time course 0hI-0hNI	0.91433	0.631
Time course 12hI-12hNI	1.00565	1
Time course 36hI-36hNI	0.88998	0.125
Time course 60hI-60hNI	0.7783	0.026

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	11.0091	0.248
transgenic ySAMdc/azygous control (red)	2.32985	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98452	0.404

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.12593	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92384	1
Manapal/WT (break)	1.03473	1
Manapal/WT (red)	1.41597	0.413