Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.11.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85691	0.389
27DAP/17DAP	1.02008	0.92
39DAP/27DAP	0.95405	0.733
41DAP/39DAP	1.09517	0.822
42DAP/41DAP	0.89481	0.774
43DAP/42DAP	0.98161	0.302
47DAP/43DAP	0.83148	0.526
52DAP/47DAP	0.88044	0.757
57DAP/52DAP	1.08398	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9534	0.224
17DAP/reference	1.15992	0.013
27DAP/reference	1.10235	0.264
39DAP/reference	1.13127	0.294
41DAP/reference	1.12151	0.093
42DAP/reference	0.90469	0.078
43DAP/reference	1.03319	0.73
47DAP/reference	0.90521	0.05
52DAP/reference	0.7269	0.071
57DAP/reference	0.77868	0.04

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10258	0.464
27DAP/17DAP	0.96134	0.878
39DAP/27DAP	0.9705	0.804
41DAP/39DAP	1.04851	1
42DAP/41DAP	1.31231	0.039
43DAP/42DAP	0.8406	0.085
47DAP/43DAP	0.92979	0.637
52DAP/47DAP	1.70823	0.228
57DAP/52DAP	1.62644	0.045
57DAP/7DAP	1.11971	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05797	0.999
17DAP/reference	1.22407	0.221
27DAP/reference	1.09109	0.551
39DAP/reference	1.33589	0.025
41DAP/reference	1.28238	0.015
42DAP/reference	1.24646	0.03
43DAP/reference	1.45272	0.045
47DAP/reference	0.9526	0.504
52DAP/reference	1.58583	0.008
57DAP/reference	1.33504	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97963	0.72
17DAP/reference	0.99748	0.747
27DAP/reference	0.82234	0.084
39DAP/reference	0.92273	0.33
41DAP/reference	0.73928	0.018
42DAP/reference	0.82547	0.121
43DAP/reference	1.06653	0.845
47DAP/reference	0.96674	0.434
52DAP/reference	0.98028	0.5
57DAP/reference	1.17959	0.314

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04938	0.846
17DAP/reference	1.11211	0.42
27DAP/reference	1.53043	0.051
39DAP/reference	1.31832	0.019
41DAP/reference	1.20221	0.57
42DAP/reference	1.28466	0.863
43DAP/reference	1.2352	0.91
47DAP/reference	0.93088	0.371
52DAP/reference	1.25619	0.216
57DAP/reference	0.62431	0.042

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10017	0.786
26DAP/20DAP	2.07769	0.798
34DAP/26DAP	2.461	1
51DAP/34DAP	1.00882	0.66
52DAP/51DAP	3.97245	0.034
53DAP/52DAP	0.54619	0.049
55DAP/53DAP	1.28399	0.185
57DAP/55DAP	0.46968	0.022
62DAP/57DAP	1.37619	0.445
68DAP/62DAP	1.6452	0.907
68DAP/14DAP	0.78351	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.32373	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.97069	0.66
Immature Eggplant/Mature Eggplant	0.63037	0.077
Ripe Pepper/Ripe Tomato	0.20722	0.224
Mature Eggplant/Ripe Tomato	0.61148	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05136	0.877
1-1-2/M82	0.92883	1
12-2/M82	0.97795
12-4/M82	1.04401	1
1-3/M82	0.70429	0.376
2-1-1/M82	1.00992	1
2-1/M82	N/A	N/A
2-6/M82	0.86422	1
3-2/M82	0.86794
4-1-1/M82	1.23914
4-1/M82	1.11113	1
4-3-2/M82	1.06813	1
4-3/M82	1.32563	1
5-3/M82	0.86437	0.364
6-2/M82	1.2409
6-3/M82	0.95022	1
7-1/M82	1.2944	0.598
7-2/M82	1.1131	0.385
9-3-2/M82	0.8646	0.449

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	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	1.11446	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.17607	0.715
DC3000/delta hrp 6h	0.93338	0.95
DC3000/delta hrp 12h	1.05965	1
DC3000/delta hrp 24h	1.10833	0.202

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.1057	0.053
DC3000 delta B/DC3000 delta AB	1.43874	0.135

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93853	1
Exp 36h	0.93244	0.661
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99805	1
Var 0h	0.299	0.332
Var 12h I row2-row1	0.89286	0.627
Var 12h NI row2-row1	1.20889	0.34
Var 36h I row2-row1	1.16515	0.742
Var 36h NI row2-row1	1.37813	0.482
Var 60h I row2-row1	0.7647	0.285
Var 60h NI row2-row1	0.9346	1
Time course 0hI-0hNI	0.91395	0.452
Time course 12hI-12hNI	1.01667	1
Time course 36hI-36hNI	1.05811	0.651
Time course 60hI-60hNI	0.93389	0.161

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)	1.2084	0.431
transgenic ySAMdc/azygous control (breaker)	0.39477	0.139
transgenic ySAMdc/azygous control (red)	1.18734	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99396	0.694

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.92935	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.78528	1
Manapal/WT (break)	0.96853	1
Manapal/WT (red)	1.29117	0.413