Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.6.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04971	0.975
27DAP/17DAP	0.96577	0.967
39DAP/27DAP	1.13043	0.992
41DAP/39DAP	1.56359	0.292
42DAP/41DAP	1.78789	0.104
43DAP/42DAP	5.24631	0.016
47DAP/43DAP	1.82878	0.187
52DAP/47DAP	0.35927	0.03
57DAP/52DAP	0.55888	0.462

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86637	0.167
17DAP/reference	0.75351	0.029
27DAP/reference	0.87705	0.201
39DAP/reference	0.96009	0.587
41DAP/reference	0.82406	0.154
42DAP/reference	1.04751	0.963
43DAP/reference	2.45438	0.006
47DAP/reference	2.61554	0.001
52DAP/reference	1.46654	0.02
57DAP/reference	1.24832	0.073

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18534	0.5
27DAP/17DAP	1.2468	0.465
39DAP/27DAP	1.37819	0.094
41DAP/39DAP	1.00364	0.997
42DAP/41DAP	17.4412	0.016
43DAP/42DAP	37.5983	0.013
47DAP/43DAP	1.54929	0.038
52DAP/47DAP	1.6992	0.145
57DAP/52DAP	0.40315	0.047
57DAP/7DAP	6.57788	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.3078	0.066
17DAP/reference	0.1715	0.011
27DAP/reference	0.22734	0.01
39DAP/reference	0.1512	0.011
41DAP/reference	0.24795	0.012
42DAP/reference	0.25789
43DAP/reference	0.33491	0.011
47DAP/reference	0.62585	0.222
52DAP/reference	0.13715	0.009
57DAP/reference	0.16004	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.69596	0.152
17DAP/reference	0.7512	0.016
27DAP/reference	0.99695	0.642
39DAP/reference	0.94456	0.348
41DAP/reference	0.90688	0.188
42DAP/reference	0.91399	0.261
43DAP/reference	0.56529	0.032
47DAP/reference	0.97916	0.512
52DAP/reference	0.79096	0.055
57DAP/reference	0.79745	0.018

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.34521	0.039
17DAP/reference	1.27682	0.374
27DAP/reference	0.20618	0.026
39DAP/reference	0.28999	0.01
41DAP/reference	0.30219	0.019
42DAP/reference	1.65434	0.017
43DAP/reference	2.65838	0.006
47DAP/reference	2.74468	0.005
52DAP/reference	2.27166	0.039
57DAP/reference	1.0796	0.771

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.14284	1
26DAP/20DAP	0.95189	1
34DAP/26DAP	1.03488	0.861
51DAP/34DAP	1.95945	0.473
52DAP/51DAP	1.09721	0.253
53DAP/52DAP	5.11667	0.021
55DAP/53DAP	1.48155	0.261
57DAP/55DAP	1.24095	0.764
62DAP/57DAP	0.64643	0.871
68DAP/62DAP	5.40354	0.557
68DAP/14DAP	0.81813

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	4.38649	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.64973	0.167
Mature Green Tomato/Ripe Tomato	0.18375	0.079
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.74702	1
Mature Eggplant/Ripe Tomato	0.06414	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	3.96982	0.526
1-1-2/M82	2.23319	1
12-2/M82	1.28868	0.955
12-4/M82	2.38348	1
1-3/M82	5.27851	0.277
2-1-1/M82	1.42336	0.689
2-1/M82	0.63678	0.74
2-6/M82	2.94374	0.385
3-2/M82	2.38826	0.549
4-1-1/M82	2.83712
4-1/M82	7.52542	0.512
4-3-2/M82	2.34721	0.262
4-3/M82	1.68389	0.268
5-3/M82	0.70254	0.49
6-2/M82	5.93881	1
6-3/M82	1.19226	1
7-1/M82	1.08519	1
7-2/M82	2.08459	0.302
9-3-2/M82	2.76401

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.98751	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.90849	1
IL12-4/WTpooled	1.02484	1
IL1-4/WTpooled	0.98684	1
WT/WTpooled	0.99239	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98665	1
DC3000/delta hrp 6h	0.771
DC3000/delta hrp 12h	0.9894	1
DC3000/delta hrp 24h	1.10969	0.383

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	7.67969

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.14653	1
Exp 36h	1.03434	1
Exp 60h	1.21193	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.7846
Var 0h	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	1.06006
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	1.03195
Var 60h NI row2-row1	0.60082	0.932
Time course 0hI-0hNI	1.0825	0.852
Time course 12hI-12hNI	1.11261	0.415
Time course 36hI-36hNI	0.84249	0.441
Time course 60hI-60hNI	1.044	0.575

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)	1.06443	0.482
transgenic ySAMdc/azygous control (breaker)	0.73888	0.251
transgenic ySAMdc/azygous control (red)	0.97567	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.2405	0.038

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.59021	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.99178	1
Manapal/WT (break)	1.2029	0.381
Manapal/WT (red)	0.80983	0.315