Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.3.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86994	0.456
27DAP/17DAP	1.22737	0.847
39DAP/27DAP	1.51042	0.825
41DAP/39DAP	1.05438	0.985
42DAP/41DAP	1.0797	0.938
43DAP/42DAP	1.15875	1
47DAP/43DAP	1.20696	0.702
52DAP/47DAP	0.95405	0.851
57DAP/52DAP	1.15598	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87824	0.128
17DAP/reference	0.81323	0.021
27DAP/reference	0.86069	0.152
39DAP/reference	0.79035	0.016
41DAP/reference	1.00656	0.814
42DAP/reference	0.93881	0.287
43DAP/reference	0.8199	0.129
47DAP/reference	1.0145	0.862
52DAP/reference	1.06118	0.407
57DAP/reference	1.11873	0.662

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90883	0.526
27DAP/17DAP	1.5148	0.128
39DAP/27DAP	1.01996	0.898
41DAP/39DAP	0.96459	0.945
42DAP/41DAP	1.02619	0.853
43DAP/42DAP	0.93826	0.576
47DAP/43DAP	0.91728	0.857
52DAP/47DAP	1.16716	0.593
57DAP/52DAP	1.60675	0.059
57DAP/7DAP	1.57461	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2112	0.555
17DAP/reference	1.0225	1
27DAP/reference	1.01665	0.698
39DAP/reference	0.86888	0.23
41DAP/reference	1.01208	0.646
42DAP/reference	0.92177	0.32
43DAP/reference	1.08859	0.569
47DAP/reference	0.67474	0.293
52DAP/reference	0.92517	0.213
57DAP/reference	0.95822	0.341

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99474	0.869
17DAP/reference	0.77433	0.018
27DAP/reference	0.96359	0.467
39DAP/reference	0.82391	0.173
41DAP/reference	0.72302	0.023
42DAP/reference	1.02707	1
43DAP/reference	0.99256	0.607
47DAP/reference	0.75472	0.015
52DAP/reference	0.8874	0.22
57DAP/reference	0.78842	0.043

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13447	0.347
17DAP/reference	0.93325	0.528
27DAP/reference	0.92662	0.302
39DAP/reference	1.01145	0.962
41DAP/reference	0.97653	0.682
42DAP/reference	1.10048	0.459
43DAP/reference	0.98924	0.738
47DAP/reference	0.87693	0.066
52DAP/reference	0.90301	0.376
57DAP/reference	1.10981	0.268

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.73814	0.355
26DAP/20DAP	0.61651
34DAP/26DAP	1.95722	1
51DAP/34DAP	4.54209
52DAP/51DAP	0.8849
53DAP/52DAP	1.02843	0.921
55DAP/53DAP	1.13116	0.634
57DAP/55DAP	0.7454	0.159
62DAP/57DAP	1.23433	0.569
68DAP/62DAP	1.27362	0.345
68DAP/14DAP	0.82723	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.66738	0.041

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.41175	1
Mature Eggplant/Ripe Tomato	1.63922	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.15112	0.694
1-3/M82	0.81983
2-1-1/M82	0.93798
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.94564
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.16644	1
6-2/M82	1.06772
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.96981
9-3-2/M82	0.9545

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.5671
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.51889
IL7-3/WTpooled	0.83676
IL12-4/WTpooled	0.96651	1
IL1-4/WTpooled	0.79152	0.834
WT/WTpooled	0.97017	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	1.05944	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96102	1
DC3000/delta hrp 6h	1.27857
DC3000/delta hrp 12h	0.78481	1
DC3000/delta hrp 24h	1.48126	0.246

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	1.21315	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03395	1
Var 0h	1.14155	0.936
Var 12h I row2-row1	1.00475
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	1.1373
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	0.98591
Var 60h NI row2-row1	1.10807
Time course 0hI-0hNI	0.85021	1
Time course 12hI-12hNI	0.89157	0.424
Time course 36hI-36hNI	1.0435	0.881
Time course 60hI-60hNI	1.5993	0.017

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)	1.04797	0.511
transgenic ySAMdc/azygous control (breaker)	1.27944	0.248
transgenic ySAMdc/azygous control (red)	0.91421	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08352	0.05

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.83432	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.82499	0.172
Manapal/WT (break)	0.94385	1
Manapal/WT (red)	1.39739	0.142