Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.1.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.44026	0.017
27DAP/17DAP	0.68624	0.11
39DAP/27DAP	1.80581	0.07
41DAP/39DAP	0.89113	0.536
42DAP/41DAP	0.85942	0.774
43DAP/42DAP	1.16141	0.763
47DAP/43DAP	0.98506	0.926
52DAP/47DAP	0.53341	0.048
57DAP/52DAP	0.82731	0.79

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.43104	0.093
17DAP/reference	1.07969	0.957
27DAP/reference	0.81043	0.129
39DAP/reference	0.96266	0.565
41DAP/reference	0.72304	0.039
42DAP/reference	1.3416	0.001
43DAP/reference	1.35857	0.016
47DAP/reference	1.08584	0.575
52DAP/reference	0.67964	0.015
57DAP/reference	0.85706	0.027

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.75328	0.075
27DAP/17DAP	1.02521	0.928
39DAP/27DAP	1.23089	0.158
41DAP/39DAP	0.87867	0.219
42DAP/41DAP	0.83905	0.203
43DAP/42DAP	1.25273	0.028
47DAP/43DAP	1.241	0.674
52DAP/47DAP	0.90696	0.413
57DAP/52DAP	1.08222	0.699
57DAP/7DAP	0.50236	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.94347	0.024
17DAP/reference	1.10151	0.092
27DAP/reference	2.51981	0.006
39DAP/reference	1.31763	0.033
41DAP/reference	1.93571	0.015
42DAP/reference	2.91357	0.006
43DAP/reference	2.0823	0.006
47DAP/reference	1.39448	0.028
52DAP/reference	1.43019	0.026
57DAP/reference	0.63211	0.011

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.51834	0.094
17DAP/reference	0.82498	0.059
27DAP/reference	1.66573	0.015
39DAP/reference	0.82877	0.097
41DAP/reference	1.03451	1
42DAP/reference	1.3531	0.011
43DAP/reference	1.1883	0.977
47DAP/reference	1.82525	0.036
52DAP/reference	0.74657	0.004
57DAP/reference	1.28666	0.085

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.4326	0.026
17DAP/reference	0.90801	0.313
27DAP/reference	1.48908	0.017
39DAP/reference	1.72108	0.01
41DAP/reference	1.09026	0.439
42DAP/reference	1.41467	0.041
43DAP/reference	1.30224	0.022
47DAP/reference	0.78861	0.005
52DAP/reference	1.25222	0.349
57DAP/reference	0.84496	0.118

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.86839	0.479
26DAP/20DAP	1.19854	0.399
34DAP/26DAP	1.03513	1
51DAP/34DAP	1.35702	0.032
52DAP/51DAP	0.81759	0.151
53DAP/52DAP	0.99519	0.99
55DAP/53DAP	0.59612	0.018
57DAP/55DAP	0.71042	0.097
62DAP/57DAP	N/A	N/A
68DAP/62DAP	1.04208	1
68DAP/14DAP	0.70141

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.75019	0.102

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.01765	1
Mature Green Tomato/Ripe Tomato	1.10462	0.437
Immature Eggplant/Mature Eggplant	3.73086	0.05
Ripe Pepper/Ripe Tomato	0.36824	0.224
Mature Eggplant/Ripe Tomato	0.07236	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.76471	0.877
1-1-2/M82	1.20211	0.977
12-2/M82	1.30215	0.448
12-4/M82	0.98201	1
1-3/M82	2.37916	0.479
2-1-1/M82	1.71571	1
2-1/M82	0.63564	0.345
2-6/M82	3.76903	0.329
3-2/M82	0.65216
4-1-1/M82	3.1232	1
4-1/M82	1.87702	1
4-3-2/M82	2.75341	0.241
4-3/M82	3.87321	0.268
5-3/M82	0.53384	0.395
6-2/M82	4.3708
6-3/M82	1.15244	1
7-1/M82	0.75997	0.408
7-2/M82	3.61559
9-3-2/M82	3.15678

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.72873	0.337
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.18795	1
IL12-4/WTpooled	0.90272	1
IL1-4/WTpooled	0.96775
WT/WTpooled	1.02331	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	1.24211	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05708	0.914
DC3000/delta hrp 6h	1.06149	1
DC3000/delta hrp 12h	1.13188	1
DC3000/delta hrp 24h	0.83869	0.053

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.46876	0.023
DC3000 delta B/DC3000 delta AB	0.49975	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.11406	1
Exp 36h	2.24124	0.489
Exp 60h	1.25012	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00225	1
Var 0h	0.92661	0.933
Var 12h I row2-row1	0.77903	0.344
Var 12h NI row2-row1	0.94486	0.494
Var 36h I row2-row1	1.01612	1
Var 36h NI row2-row1	1.26991	0.482
Var 60h I row2-row1	1.13561	0.562
Var 60h NI row2-row1	1.01521	1
Time course 0hI-0hNI	0.98559	0.973
Time course 12hI-12hNI	0.98748	0.953
Time course 36hI-36hNI	0.84744	0.029
Time course 60hI-60hNI	0.23724	0.005

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)	0.66075	0.391
transgenic ySAMdc/azygous control (breaker)	0.44068	0.142
transgenic ySAMdc/azygous control (red)	1.76966	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.1398	0.089

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.56032	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.09046	1
Manapal/WT (break)	1.00907	1
Manapal/WT (red)	1.42073	0.164