Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.6.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15805	0.876
27DAP/17DAP	1.88696	0.274
39DAP/27DAP	1.32556	0.507
41DAP/39DAP	1.20078	0.511
42DAP/41DAP	1.25429	0.671
43DAP/42DAP	1.18964	0.861
47DAP/43DAP	1.67778	0.349
52DAP/47DAP	1.3163	0.608
57DAP/52DAP	1.43931	0.677

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91079	0.162
17DAP/reference	1.02829	0.148
27DAP/reference	1.01861	0.82
39DAP/reference	0.98689	0.828
41DAP/reference	0.9123	0.341
42DAP/reference	0.88302	0.012
43DAP/reference	1.02413	0.787
47DAP/reference	0.84989	0.014
52DAP/reference	0.7444	0.067
57DAP/reference	0.84631	0.031

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.52928	0.053
27DAP/17DAP	1.50222	0.033
39DAP/27DAP	1.3782	0.236
41DAP/39DAP	0.69139	0.104
42DAP/41DAP	1.49985	0.015
43DAP/42DAP	1.455	0.014
47DAP/43DAP	1.03431	0.939
52DAP/47DAP	1.32346	0.317
57DAP/52DAP	1.16049	0.479
57DAP/7DAP	2.60555	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8621	0.183
17DAP/reference	0.82738	0.094
27DAP/reference	1.06597	0.371
39DAP/reference	0.98349	0.552
41DAP/reference	0.87951	0.122
42DAP/reference	0.95728	0.289
43DAP/reference	0.86123	0.019
47DAP/reference	0.89839	0.128
52DAP/reference	0.98692	0.679
57DAP/reference	0.8395	0.015

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07153	0.582
17DAP/reference	0.9731	0.461
27DAP/reference	0.849	0.15
39DAP/reference	0.84021	0.054
41DAP/reference	0.80922	0.056
42DAP/reference	0.86528	0.042
43DAP/reference	0.94712	0.468
47DAP/reference	0.89508	0.047
52DAP/reference	0.93767	0.259
57DAP/reference	1.07455	0.755

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85095	0.057
17DAP/reference	0.98399	0.696
27DAP/reference	0.8384	0.085
39DAP/reference	0.87187	0.133
41DAP/reference	0.90119	0.237
42DAP/reference	1.02017	0.816
43DAP/reference	1.01648	0.639
47DAP/reference	0.94408	0.357
52DAP/reference	1.13883	0.369
57DAP/reference	0.81246	0.122

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06863	0.966
26DAP/20DAP	1.36769	0.176
34DAP/26DAP	1.38999	0.542
51DAP/34DAP	1.40478	0.121
52DAP/51DAP	1.05447	0.836
53DAP/52DAP	0.71952	0.049
55DAP/53DAP	0.72633	0.029
57DAP/55DAP	1.55063	0.311
62DAP/57DAP	1.13011	0.902
68DAP/62DAP	0.96804	0.7
68DAP/14DAP	0.88712	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.85452	0.253

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.54991	0.018
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.48197	1
Mature Eggplant/Ripe Tomato	1.26301

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.2002	0.591
1-1-2/M82	0.96482	1
12-2/M82	1.03418	1
12-4/M82	0.87022	0.619
1-3/M82	1.2277	1
2-1-1/M82	0.54878	0.465
2-1/M82	0.84956	0.519
2-6/M82	0.75526	1
3-2/M82	N/A	N/A
4-1-1/M82	0.70767	1
4-1/M82	0.88521
4-3-2/M82	0.6105	0.487
4-3/M82	0.98664	1
5-3/M82	1.14879	1
6-2/M82	0.75851	0.481
6-3/M82	1.11457	1
7-1/M82	0.81134
7-2/M82	0.82148	0.578
9-3-2/M82	0.81634	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.07702	0.659
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.04295	1
IL12-4/WTpooled	1.08182	0.695
IL1-4/WTpooled	1.01644
WT/WTpooled	1.05319	0.686

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	1.21637	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09769	0.692
DC3000/delta hrp 6h	0.89747	0.95
DC3000/delta hrp 12h	1.06175	1
DC3000/delta hrp 24h	0.41369	0.039

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.38614
DC3000 delta B/DC3000 delta AB	0.80406

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.8073	1
Exp 36h	0.64181	0.374
Exp 60h	0.60004	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99713	1
Var 0h	1.00231	1
Var 12h I row2-row1	1.23833	0.443
Var 12h NI row2-row1	1.0299	0.34
Var 36h I row2-row1	0.95912	1
Var 36h NI row2-row1	1.22906	1
Var 60h I row2-row1	0.88804	0.306
Var 60h NI row2-row1	1.08922	0.904
Time course 0hI-0hNI	1.17464	0.451
Time course 12hI-12hNI	1.18764	0.087
Time course 36hI-36hNI	0.78459	0.023
Time course 60hI-60hNI	0.90527	0.319

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)	0.94499	0.567
transgenic ySAMdc/azygous control (breaker)	1.02714	1
transgenic ySAMdc/azygous control (red)	1.27565	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01303	0.301

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.05393	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.09932	1
Manapal/WT (red)	0.92575	0.607