Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.19.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.56631	0.128
27DAP/17DAP	1.29127	0.801
39DAP/27DAP	1.27945	0.52
41DAP/39DAP	1.16863	0.973
42DAP/41DAP	1.41409	0.133
43DAP/42DAP	0.99089	0.931
47DAP/43DAP	1.12457	0.825
52DAP/47DAP	0.93241	0.806
57DAP/52DAP	1.29813	0.894

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14094	0.35
17DAP/reference	0.93454	0.321
27DAP/reference	0.96509	0.581
39DAP/reference	1.06651	0.747
41DAP/reference	0.8936	0.267
42DAP/reference	1.04668	0.869
43DAP/reference	0.95399	0.41
47DAP/reference	1.15608	0.048
52DAP/reference	1.3791	0.014
57DAP/reference	1.26066	0.018

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.76679	0.547
27DAP/17DAP	1.20555	0.413
39DAP/27DAP	0.93833	0.607
41DAP/39DAP	1.60784	0.169
42DAP/41DAP	0.88811	0.377
43DAP/42DAP	1.28252	0.478
47DAP/43DAP	0.97101	0.843
52DAP/47DAP	1.25278	0.734
57DAP/52DAP	1.41052	0.911
57DAP/7DAP	1.30224	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23883	0.144
17DAP/reference	1.09417	0.574
27DAP/reference	1.03265	0.974
39DAP/reference	1.02685	1
41DAP/reference	1.00217	0.709
42DAP/reference	0.98096	0.554
43DAP/reference	1.31783	0.016
47DAP/reference	1.16419	0.214
52DAP/reference	0.98302	0.523
57DAP/reference	1.03622	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02577	0.97
17DAP/reference	0.97685	0.576
27DAP/reference	1.09884	0.583
39DAP/reference	1.26982	0.106
41DAP/reference	1.26475	0.048
42DAP/reference	1.29956	0.008
43DAP/reference	0.92388	0.352
47DAP/reference	1.18216	0.081
52DAP/reference	1.09066	0.3
57DAP/reference	0.97752	0.581

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9893	0.653
17DAP/reference	0.9203	0.328
27DAP/reference	1.09912	0.149
39DAP/reference	1.01082	1
41DAP/reference	1.00026	0.826
42DAP/reference	0.99985	0.816
43DAP/reference	1.12244	0.336
47DAP/reference	0.88912	0.153
52DAP/reference	2.26132	0.228
57DAP/reference	1.54628	0.061

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0048	1
26DAP/20DAP	1.12015	0.785
34DAP/26DAP	0.91261	0.783
51DAP/34DAP	0.67398	0.274
52DAP/51DAP	0.99265	1
53DAP/52DAP	1.5123	0.319
55DAP/53DAP	1.22072	0.608
57DAP/55DAP	0.95534	0.757
62DAP/57DAP	0.85691	0.466
68DAP/62DAP	1.08295	0.939
68DAP/14DAP	1.562	0.027

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.85541	0.239

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.24514	0.113
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	2.88557	0.05
Ripe Pepper/Ripe Tomato	1.35549	1
Mature Eggplant/Ripe Tomato	1.64306

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	N/A	N/A
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	N/A	N/A
3-2/M82	N/A	N/A
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	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.9806	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.18221
IL1-4/WTpooled	1.63127	1
WT/WTpooled	1.75213	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	1.38907

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0197	1
DC3000/delta hrp 6h	1.11677	1
DC3000/delta hrp 12h	0.93859	1
DC3000/delta hrp 24h	1.48204	0.165

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.82816	0.042
DC3000 delta B/DC3000 delta AB	1.87963	0.069

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.94489	1
Exp 36h	1.49641	1
Exp 60h	1.79983	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.2826	1
Var 0h	3.93642
Var 12h I row2-row1	1.11442	0.736
Var 12h NI row2-row1	1.98379	1
Var 36h I row2-row1	1.12608	0.601
Var 36h NI row2-row1	0.59345	1
Var 60h I row2-row1	0.95841	0.952
Var 60h NI row2-row1	0.4568	1
Time course 0hI-0hNI	1.38992	0.833
Time course 12hI-12hNI	1.31323	0.698
Time course 36hI-36hNI	2.18222	0.039
Time course 60hI-60hNI	6.40657	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)	0.96516	0.722
transgenic ySAMdc/azygous control (breaker)	0.72216	0.173
transgenic ySAMdc/azygous control (red)	1.1228	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.09615	0.13

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.66718	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.99818	1
Manapal/WT (break)	1.14579	1
Manapal/WT (red)	0.98009	0.863