Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.15.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90814	0.586
27DAP/17DAP	1.02131	1
39DAP/27DAP	1.63515	0.83
41DAP/39DAP	1.6068	0.185
42DAP/41DAP	2.97593	0.016
43DAP/42DAP	1.75764	0.772
47DAP/43DAP	0.93511	0.76
52DAP/47DAP	0.53225	0.048
57DAP/52DAP	1.09873	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.234	0.089
17DAP/reference	1.12515	0.318
27DAP/reference	1.03051	1
39DAP/reference	1.11159	0.256
41DAP/reference	0.94126	0.341
42DAP/reference	1.02519	0.707
43DAP/reference	1.10217	0.547
47DAP/reference	0.99698	0.602
52DAP/reference	1.01795	0.73
57DAP/reference	0.88236	0.176

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22343	0.05
27DAP/17DAP	1.01849	0.957
39DAP/27DAP	1.83642	0.047
41DAP/39DAP	0.61603	0.043
42DAP/41DAP	2.27039	0.002
43DAP/42DAP	4.03135	0.014
47DAP/43DAP	1.01473	0.989
52DAP/47DAP	1.25596	0.543
57DAP/52DAP	0.65308	0.141
57DAP/7DAP	3.05356	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98297	0.613
17DAP/reference	0.86342	0.056
27DAP/reference	0.82399	0.062
39DAP/reference	0.92802	0.23
41DAP/reference	0.97307	0.469
42DAP/reference	0.93451	0.289
43DAP/reference	0.94853	0.385
47DAP/reference	0.80833	0.079
52DAP/reference	0.83028	0.09
57DAP/reference	0.90775	0.109

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94052	0.564
17DAP/reference	1.15213	0.385
27DAP/reference	1.01196	0.735
39DAP/reference	1.13176	0.556
41DAP/reference	1.16013	0.48
42DAP/reference	1.01414	1
43DAP/reference	1.05756	0.875
47DAP/reference	1.00709	0.714
52DAP/reference	1.14366	0.498
57DAP/reference	0.97244	0.581

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85798	0.183
17DAP/reference	1.07177	0.977
27DAP/reference	0.86598	0.155
39DAP/reference	0.88318	0.299
41DAP/reference	0.81837	0.107
42DAP/reference	1.00296	0.671
43DAP/reference	0.86737	0.216
47DAP/reference	1.18801	0.265
52DAP/reference	0.87442	0.472
57DAP/reference	0.98183	0.652

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.80962	0.807
26DAP/20DAP	0.9409	1
34DAP/26DAP	0.97188	0.972
51DAP/34DAP	0.96836	0.779
52DAP/51DAP	0.99063	1
53DAP/52DAP	1.0305	0.938
55DAP/53DAP	1.02765	1
57DAP/55DAP	1.33257	0.805
62DAP/57DAP	0.99782	1
68DAP/62DAP	1.01185	0.939
68DAP/14DAP	0.59866	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	9.5549	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.41709	0.019
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.46327	0.224
Mature Eggplant/Ripe Tomato	0.5887	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.28011	0.591
1-1-2/M82	1.25019	1
12-2/M82	0.92321	0.955
12-4/M82	1.87221	1
1-3/M82	1.18138	0.479
2-1-1/M82	1.3476	0.375
2-1/M82	0.87705	0.74
2-6/M82	1.24442
3-2/M82	0.85885	1
4-1-1/M82	1.13833	0.968
4-1/M82	2.25434	1
4-3-2/M82	1.3524	1
4-3/M82	1.17797	1
5-3/M82	0.99538	1
6-2/M82	1.2784
6-3/M82	0.89955	1
7-1/M82	1.14642
7-2/M82	1.14551	0.324
9-3-2/M82	1.78291	0.196

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	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.33734	0.71
IL1-4/WTpooled	2.09761
WT/WTpooled	0.74162	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	0.84337	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01599	0.921
DC3000/delta hrp 6h	1.18657	1
DC3000/delta hrp 12h	1.02798	1
DC3000/delta hrp 24h	0.86173	0.264

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.86357	0.093
DC3000 delta B/DC3000 delta AB	0.99085	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9312	1
Exp 36h	0.79102	0.374
Exp 60h	0.7477	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98909	1
Var 0h	0.95516	1
Var 12h I row2-row1	0.80862	0.353
Var 12h NI row2-row1	1.21043	0.34
Var 36h I row2-row1	1.27617	0.601
Var 36h NI row2-row1	0.74587	0.549
Var 60h I row2-row1	1.1994	1
Var 60h NI row2-row1	0.86137	0.866
Time course 0hI-0hNI	1.02423	0.867
Time course 12hI-12hNI	0.98126	0.886
Time course 36hI-36hNI	1.17353	0.009
Time course 60hI-60hNI	0.76993	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)	1.04345	0.541
transgenic ySAMdc/azygous control (breaker)	1.45136	0.166
transgenic ySAMdc/azygous control (red)	1.03464	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.90393	0.042

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.66111	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.83583	0.088
Manapal/WT (break)	1.45581	0.126
Manapal/WT (red)	1.21511	0.222