Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.11.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.46505	0.709
27DAP/17DAP	1.65593	0.401
39DAP/27DAP	1.3228	0.524
41DAP/39DAP	0.79211	0.279
42DAP/41DAP	1.42379	0.397
43DAP/42DAP	0.97001	0.912
47DAP/43DAP	0.87365	0.613
52DAP/47DAP	0.88935	0.682
57DAP/52DAP	0.94167	0.926

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3829	0.018
17DAP/reference	1.0718	0.33
27DAP/reference	1.12796	0.394
39DAP/reference	1.10531	0.413
41DAP/reference	1.06305	0.48
42DAP/reference	1.33125	0.001
43DAP/reference	0.97952	0.728
47DAP/reference	0.86004	0.05
52DAP/reference	0.85458	0.065
57DAP/reference	0.93177	0.277

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	3.79123	0.039
27DAP/17DAP	0.73295	0.312
39DAP/27DAP	2.00302	0.067
41DAP/39DAP	0.88472	0.63
42DAP/41DAP	1.16662	0.601
43DAP/42DAP	1.14319	0.513
47DAP/43DAP	0.99009	0.954
52DAP/47DAP	0.95346	0.837
57DAP/52DAP	0.79115	0.209
57DAP/7DAP	1.80259	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20473	0.177
17DAP/reference	1.49865	0.008
27DAP/reference	1.32685	0.301
39DAP/reference	1.78719	0.006
41DAP/reference	1.67178	0.025
42DAP/reference	1.60076	0.009
43DAP/reference	1.70336	0.008
47DAP/reference	1.36681	0.075
52DAP/reference	1.56959	0.013
57DAP/reference	1.7344	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14817	0.65
17DAP/reference	1.26427	0.171
27DAP/reference	1.13424	0.735
39DAP/reference	1.19532	0.657
41DAP/reference	1.29115	0.146
42DAP/reference	1.1645	0.115
43DAP/reference	1.33861	0.105
47DAP/reference	1.54822	0.022
52DAP/reference	1.05896	0.761
57DAP/reference	1.78757	0.025

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14725	0.456
17DAP/reference	1.09046	0.784
27DAP/reference	1.59248	0.033
39DAP/reference	1.49344	0.052
41DAP/reference	1.2581	0.125
42DAP/reference	1.05135	0.701
43DAP/reference	1.16068	0.634
47DAP/reference	1.05801	1
52DAP/reference	1.67633	0.041
57DAP/reference	1.0209	0.73

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95088	1
26DAP/20DAP	0.7134	0.317
34DAP/26DAP	0.87156	0.675
51DAP/34DAP	1.72911	0.039
52DAP/51DAP	0.74566	0.151
53DAP/52DAP	1.1884	0.154
55DAP/53DAP	0.47527	0.021
57DAP/55DAP	0.69264	0.099
62DAP/57DAP	4.64018	0.006
68DAP/62DAP	1.05564	0.722
68DAP/14DAP	1.01351	0.85

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.94142	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.86072	0.41
Mature Green Tomato/Ripe Tomato	1.35221	0.048
Immature Eggplant/Mature Eggplant	0.79261
Ripe Pepper/Ripe Tomato	1.69872	1
Mature Eggplant/Ripe Tomato	1.94885	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.87222	0.934
1-1-2/M82	1.07638	1
12-2/M82	2.01797
12-4/M82	1.68371	1
1-3/M82	2.83146	0.255
2-1-1/M82	0.71092	0.683
2-1/M82	0.86714	0.325
2-6/M82	0.8928	1
3-2/M82	1.31421	0.426
4-1-1/M82	0.55861
4-1/M82	1.18317	1
4-3-2/M82	1.23763	0.508
4-3/M82	0.86168	0.72
5-3/M82	0.84064	0.447
6-2/M82	N/A	N/A
6-3/M82	1.01892	1
7-1/M82	1.16119
7-2/M82	0.94971	1
9-3-2/M82	1.19109

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.65439	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.04137	1
IL12-4/WTpooled	0.83449	0.581
IL1-4/WTpooled	0.95639	1
WT/WTpooled	1.04683	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	1.47321	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.18394	0.875
DC3000/delta hrp 6h	1.04083	0.95
DC3000/delta hrp 12h	1.04724	1
DC3000/delta hrp 24h	1.17756	0.84

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.85173	0.023
DC3000 delta B/DC3000 delta AB	1.14308	0.296

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.20071	1
Exp 36h	1.28644	0.371
Exp 60h	1.3343	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03666	1
Var 0h	0.95008	1
Var 12h I row2-row1	1.3082	0.58
Var 12h NI row2-row1	1.70455	0.281
Var 36h I row2-row1	1.27501	0.298
Var 36h NI row2-row1	0.73161	0.522
Var 60h I row2-row1	0.58348	0.285
Var 60h NI row2-row1	0.8887	0.866
Time course 0hI-0hNI	1.31229	0.262
Time course 12hI-12hNI	1.06868	0.73
Time course 36hI-36hNI	1.32291	0.101
Time course 60hI-60hNI	6.57869	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)	0.90853	0.485
transgenic ySAMdc/azygous control (breaker)	0.74941	0.173
transgenic ySAMdc/azygous control (red)	1.07129	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1	0.967

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.4456	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.95115	1
Manapal/WT (break)	0.48335	0.333
Manapal/WT (red)	0.65164	0.181