Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.19.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.54455	0.891
27DAP/17DAP	2.57563	0.42
39DAP/27DAP	1.01576	0.84
41DAP/39DAP	0.92292	0.558
42DAP/41DAP	1.17053	0.903
43DAP/42DAP	0.94365	0.877
47DAP/43DAP	0.7924	0.355
52DAP/47DAP	2.18156	0.198
57DAP/52DAP	0.83206	0.845

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79414	0.055
17DAP/reference	0.72091	0.007
27DAP/reference	0.78813	0.015
39DAP/reference	0.74035	0.013
41DAP/reference	0.70706	0.01
42DAP/reference	1.21367	0.011
43DAP/reference	0.7637	0.103
47DAP/reference	0.94697	0.279
52DAP/reference	1.01885	0.791
57DAP/reference	1.0769	0.355

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.2497	0.63
27DAP/17DAP	1.05392	0.967
39DAP/27DAP	0.90463	0.536
41DAP/39DAP	1.5351	0.284
42DAP/41DAP	0.76847	0.113
43DAP/42DAP	1.4827	0.025
47DAP/43DAP	1.37956	0.444
52DAP/47DAP	1.3646	0.39
57DAP/52DAP	1.55944	0.276
57DAP/7DAP	1.26782	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89726	0.224
17DAP/reference	0.99185	0.599
27DAP/reference	0.89682	0.159
39DAP/reference	0.90307	0.109
41DAP/reference	1.21255	0.35
42DAP/reference	0.88108	0.151
43DAP/reference	1.72509	0.007
47DAP/reference	0.94958	0.383
52DAP/reference	1.30594	0.046
57DAP/reference	2.39298	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78559	0.045
17DAP/reference	0.83198	0.075
27DAP/reference	0.83582	0.108
39DAP/reference	0.92921	0.281
41DAP/reference	1.26569	0.021
42DAP/reference	0.94835	0.355
43DAP/reference	0.79647	0.075
47DAP/reference	0.92488	0.107
52DAP/reference	0.8269	0.029
57DAP/reference	0.81155	0.046

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.72615	0.035
17DAP/reference	0.96407	0.579
27DAP/reference	1.02682	0.621
39DAP/reference	1.09009	0.33
41DAP/reference	0.99044	0.682
42DAP/reference	0.98205	0.671
43DAP/reference	1.10599	0.25
47DAP/reference	1.0882	0.82
52DAP/reference	1.52143	0.118
57DAP/reference	1.5028	0.033

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93118	1
26DAP/20DAP	0.99931	1
34DAP/26DAP	1.66981	0.819
51DAP/34DAP	0.92019	0.722
52DAP/51DAP	1.51807	0.454
53DAP/52DAP	1.52693	0.643
55DAP/53DAP	1.15666	0.452
57DAP/55DAP	2.26086	0.87
62DAP/57DAP	0.86253	0.466
68DAP/62DAP	1.5001	0.02
68DAP/14DAP	1.95793	0.043

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.59235	0.122

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.44004	0.081
Mature Green Tomato/Ripe Tomato	0.15849	0.018
Immature Eggplant/Mature Eggplant	1.1442	0.248
Ripe Pepper/Ripe Tomato	0.51839	0.224
Mature Eggplant/Ripe Tomato	0.44013	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.41337
12-2/M82	4.65236
12-4/M82	0.59245
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	0.79017
3-2/M82	N/A	N/A
4-1-1/M82	2.50788
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.27596	1
5-3/M82	0.31623	0.419
6-2/M82	6.0323	0.253
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.68138
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	0.47867
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.28458	0.516
IL1-4/WTpooled	0.87573	0.389
WT/WTpooled	1.0664	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	1.87349	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99853	1
DC3000/delta hrp 6h	1.02736	0.95
DC3000/delta hrp 12h	0.96497	1
DC3000/delta hrp 24h	1.65267	0.158

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	0.50053

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.25188	1
Exp 36h	1.39106	0.489
Exp 60h	1.90297	0.18

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96975	1
Var 0h	0.93382	0.933
Var 12h I row2-row1	0.94306	0.948
Var 12h NI row2-row1	1.33467	1
Var 36h I row2-row1	1.18315	1
Var 36h NI row2-row1	0.62932	1
Var 60h I row2-row1	0.89217	0.582
Var 60h NI row2-row1	0.54639	1
Time course 0hI-0hNI	1.29472	0.852
Time course 12hI-12hNI	1.40563	0.593
Time course 36hI-36hNI	4.34273	0.008
Time course 60hI-60hNI	16.2448	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)	1.60752	0.397
transgenic ySAMdc/azygous control (breaker)	0.47784	0.134
transgenic ySAMdc/azygous control (red)	1.05846	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.13703	0.142

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.1242	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.66505	0.172
Manapal/WT (break)	0.79123	1
Manapal/WT (red)	0.64795	0.242