Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.15.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22539	0.602
27DAP/17DAP	1.17762	0.849
39DAP/27DAP	1.36586	0.372
41DAP/39DAP	1.01616	0.922
42DAP/41DAP	0.93546	1
43DAP/42DAP	1.01787	0.937
47DAP/43DAP	1.3282	0.733
52DAP/47DAP	1.03208	0.916
57DAP/52DAP	1.05191	0.995

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91187	0.177
17DAP/reference	0.86981	0.021
27DAP/reference	1.05661	0.672
39DAP/reference	0.88025	0.044
41DAP/reference	0.83482	0.114
42DAP/reference	0.92802	0.12
43DAP/reference	0.9065	0.063
47DAP/reference	0.98685	0.503
52DAP/reference	1.04608	0.548
57DAP/reference	1.03527	0.762

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99025	0.782
27DAP/17DAP	1.02496	0.969
39DAP/27DAP	0.99692	1
41DAP/39DAP	1.10585	0.455
42DAP/41DAP	1.02472	0.935
43DAP/42DAP	0.96198	0.447
47DAP/43DAP	1.00604	0.957
52DAP/47DAP	0.91929	0.439
57DAP/52DAP	0.8988	0.258
57DAP/7DAP	0.83969	0.145

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92257	0.326
17DAP/reference	1.02078	1
27DAP/reference	1.0731	0.16
39DAP/reference	1.15309	0.086
41DAP/reference	1.208	0.303
42DAP/reference	1.24028	0.233
43DAP/reference	1.07781	0.483
47DAP/reference	0.96349	0.504
52DAP/reference	1.15421	0.062
57DAP/reference	1.05467	0.799

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10572	0.193
17DAP/reference	0.93459	0.389
27DAP/reference	0.91133	0.167
39DAP/reference	0.92483	0.105
41DAP/reference	0.93418	0.291
42DAP/reference	0.94787	0.355
43DAP/reference	1.04155	0.899
47DAP/reference	1.01609	1
52DAP/reference	0.95769	0.302
57DAP/reference	1.04251	0.755

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93161	0.23
17DAP/reference	0.99934	0.825
27DAP/reference	0.89318	0.174
39DAP/reference	0.9296	0.122
41DAP/reference	0.99076	0.682
42DAP/reference	1.07003	0.775
43DAP/reference	0.96775	0.545
47DAP/reference	1.00511	0.731
52DAP/reference	0.95136	0.505
57DAP/reference	1.05837	0.909

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.2058	1
26DAP/20DAP	0.9283	1
34DAP/26DAP	1.08007	0.304
51DAP/34DAP	0.92385	0.442
52DAP/51DAP	1.05338	0.842
53DAP/52DAP	0.99328	0.978
55DAP/53DAP	0.89341	0.243
57DAP/55DAP	0.87753	0.59
62DAP/57DAP	1.04372	0.8
68DAP/62DAP	0.99122	0.863
68DAP/14DAP	1.07606	0.802

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.03948	0.74

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.77017	0.055
Immature Eggplant/Mature Eggplant	3.82992	0.069
Ripe Pepper/Ripe Tomato	0.51067	0.293
Mature Eggplant/Ripe Tomato	13.8344	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99823	1
1-1-2/M82	0.7999	1
12-2/M82	1.27178
12-4/M82	1.17432	1
1-3/M82	0.81625	0.501
2-1-1/M82	1.00468	1
2-1/M82	N/A	N/A
2-6/M82	1	1
3-2/M82	0.86496	1
4-1-1/M82	1.43503
4-1/M82	2.04219
4-3-2/M82	0.96745	0.487
4-3/M82	0.79215
5-3/M82	1.05048	1
6-2/M82	N/A	N/A
6-3/M82	1.25863	0.971
7-1/M82	1.04399
7-2/M82	0.7478	0.796
9-3-2/M82	0.91192	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.13987	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.09347	0.792
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.02742	1
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	1.27735	0.139

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08385	0.823
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.23212	1
DC3000/delta hrp 24h	1.21929	0.567

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.14684	0.121
DC3000 delta B/DC3000 delta AB	1.12175	0.308

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.8126	1
Exp 36h	1.64735	0.693
Exp 60h	1.81239	0.221

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02111	1
Var 0h	1.92956	0.936
Var 12h I row2-row1	1.26675	0.506
Var 12h NI row2-row1	0.96314	0.906
Var 36h I row2-row1	0.90141	0.805
Var 36h NI row2-row1	1.23581	1
Var 60h I row2-row1	1.09211	0.562
Var 60h NI row2-row1	1.03678	1
Time course 0hI-0hNI	0.97869	0.922
Time course 12hI-12hNI	1.08463	0.536
Time course 36hI-36hNI	1.18179	0.248
Time course 60hI-60hNI	1.24892	0.009

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)	1.04043	0.571
transgenic ySAMdc/azygous control (breaker)	0.83901	0.142
transgenic ySAMdc/azygous control (red)	1.09123	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93306	0.085

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01109	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.19858	0.14
Manapal/WT (break)	0.81312	0.333
Manapal/WT (red)	0.77575	0.424