Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.16.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.6692	0.142
27DAP/17DAP	1.52033	0.544
39DAP/27DAP	2.31282	0.672
41DAP/39DAP	2.40857	0.483
42DAP/41DAP	0.97028	1
43DAP/42DAP	1.27122	0.937
47DAP/43DAP	0.22437	0.04
52DAP/47DAP	0.82458	0.554
57DAP/52DAP	0.66234	0.503

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.71196	0.03
17DAP/reference	0.68729	0.01
27DAP/reference	0.90864	0.304
39DAP/reference	0.70757	0.016
41DAP/reference	0.73931	0.039
42DAP/reference	1.28679	0.008
43DAP/reference	0.81108	0.049
47DAP/reference	0.91557	0.148
52DAP/reference	0.97243	0.489
57DAP/reference	1.08259	0.105

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.54477	0.087
27DAP/17DAP	0.9494	0.878
39DAP/27DAP	4.953	0.035
41DAP/39DAP	5.58485	0.005
42DAP/41DAP	0.54472	0.007
43DAP/42DAP	0.32254	0.022
47DAP/43DAP	1.0339	0.914
52DAP/47DAP	1.54722	0.982
57DAP/52DAP	0.54999	0.206
57DAP/7DAP	1.26236	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74761	0.088
17DAP/reference	0.93458	0.253
27DAP/reference	1.49822	0.01
39DAP/reference	0.85451	0.073
41DAP/reference	1.00062	0.741
42DAP/reference	1.14812	0.046
43DAP/reference	0.85887	0.016
47DAP/reference	1.30432	0.395
52DAP/reference	1.00599	1
57DAP/reference	0.85052	0.061

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.60022	0.005
17DAP/reference	0.7502	0.007
27DAP/reference	0.85324	0.069
39DAP/reference	1.49432	0.099
41DAP/reference	1.37058	0.05
42DAP/reference	1.3171	0.148
43DAP/reference	1.90345	0.15
47DAP/reference	1.82977	0.03
52DAP/reference	1.04238	0.629
57DAP/reference	2.26306	0.008

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13172	0.918
17DAP/reference	1.00625	0.81
27DAP/reference	0.77211	0.034
39DAP/reference	0.84115	0.033
41DAP/reference	1.13295	0.249
42DAP/reference	1.30131	0.017
43DAP/reference	0.8963	0.246
47DAP/reference	0.76247	0.008
52DAP/reference	1.0069	0.821
57DAP/reference	1.38409	0.104

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.89213	1
26DAP/20DAP	1.00791	1
34DAP/26DAP	1.44137	0.819
51DAP/34DAP	0.86397
52DAP/51DAP	1.21023	0.708
53DAP/52DAP	0.98324	0.924
55DAP/53DAP	0.99264	0.807
57DAP/55DAP	0.60581	0.047
62DAP/57DAP	1.0911	0.935
68DAP/62DAP	1.73923	0.242
68DAP/14DAP	2.50058	0.131

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	5.75045	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	12.2009	0.015
Immature Eggplant/Mature Eggplant	1.84506
Ripe Pepper/Ripe Tomato	0.45373
Mature Eggplant/Ripe Tomato	0.57642	0.234

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	2.76359
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	3.75579	0.508
4-3/M82	N/A	N/A
5-3/M82	2.191
6-2/M82	6.79763
6-3/M82	N/A	N/A
7-1/M82	0.80559
7-2/M82	N/A	N/A
9-3-2/M82	3.28709	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.96178	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.25992	0.362
IL12-4/WTpooled	1.1212	0.624
IL1-4/WTpooled	0.98783
WT/WTpooled	0.97457	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	2.20222	0.084

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.88557	0.941
DC3000/delta hrp 6h	0.98983	0.95
DC3000/delta hrp 12h	0.99836	1
DC3000/delta hrp 24h	2.02201	0.025

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.17109	0.042
DC3000 delta B/DC3000 delta AB	4.68829	0.02

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	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	0.98924	1
Var 0h	0.79467	0.457
Var 12h I row2-row1	1.0067	1
Var 12h NI row2-row1	2.8186	0.165
Var 36h I row2-row1	1.38175	1
Var 36h NI row2-row1	0.43322	0.478
Var 60h I row2-row1	0.88505	0.285
Var 60h NI row2-row1	0.61483	0.483
Time course 0hI-0hNI	1.9874	0.63
Time course 12hI-12hNI	1.99075	0.536
Time course 36hI-36hNI	9.767	0.004
Time course 60hI-60hNI	140.964	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)	0.37027	0.246
transgenic ySAMdc/azygous control (breaker)	0.5656	0.131
transgenic ySAMdc/azygous control (red)	1.03187	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98471	0.5

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.23699	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.40984	1
Manapal/WT (break)	0.40937	0.333
Manapal/WT (red)	0.40723	0.216