Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.19.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.43328	0.166
27DAP/17DAP	1.12496	0.883
39DAP/27DAP	0.97495	0.719
41DAP/39DAP	0.87382	0.501
42DAP/41DAP	0.94679	1
43DAP/42DAP	1.03258	1
47DAP/43DAP	0.99822	0.959
52DAP/47DAP	1.24856	0.665
57DAP/52DAP	1.01884	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00435	0.661
17DAP/reference	0.9703	0.597
27DAP/reference	1.09349	0.457
39DAP/reference	0.88326	0.068
41DAP/reference	0.88387	0.085
42DAP/reference	1.05832	0.931
43DAP/reference	0.98672	0.763
47DAP/reference	1.14063	0.391
52DAP/reference	1.54199	0.096
57DAP/reference	1.39862	0.022

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99892	0.847
27DAP/17DAP	1.1268	0.576
39DAP/27DAP	0.94878	0.703
41DAP/39DAP	1.02412	0.883
42DAP/41DAP	0.98884	0.84
43DAP/42DAP	0.77653	0.085
47DAP/43DAP	0.86302	0.31
52DAP/47DAP	1.12566	0.63
57DAP/52DAP	1.41429	0.155
57DAP/7DAP	1.08425	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01195	1
17DAP/reference	0.8763	0.108
27DAP/reference	1.01318	0.748
39DAP/reference	1.01049	1
41DAP/reference	1.06296	0.891
42DAP/reference	0.88697	0.144
43DAP/reference	1.06055	1
47DAP/reference	0.96068	0.671
52DAP/reference	1.03085	1
57DAP/reference	0.96444	0.458

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87602	0.222
17DAP/reference	0.8874	0.201
27DAP/reference	1.24201	0.38
39DAP/reference	1.41415	0.041
41DAP/reference	1.51928	0.011
42DAP/reference	1.25007	0.016
43DAP/reference	1.01035	0.748
47DAP/reference	0.96927	0.459
52DAP/reference	0.98576	0.407
57DAP/reference	0.8792	0.169

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11625	0.23
17DAP/reference	0.97446	0.668
27DAP/reference	1.03399	0.871
39DAP/reference	0.88499	0.063
41DAP/reference	0.95382	0.264
42DAP/reference	1.38382	0.258
43DAP/reference	1.30226	0.202
47DAP/reference	1.19345	0.339
52DAP/reference	0.90218	0.334
57DAP/reference	1.56208	0.245

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.5005	0.945
26DAP/20DAP	1.14316	0.635
34DAP/26DAP	1.32303	0.542
51DAP/34DAP	1.64404	0.677
52DAP/51DAP	1.62246	0.068
53DAP/52DAP	0.94322	0.797
55DAP/53DAP	1.52838	0.055
57DAP/55DAP	0.82345	0.49
62DAP/57DAP	0.80237	0.28
68DAP/62DAP	1.39523	0.464
68DAP/14DAP	1.34	0.211

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.43315	0.099

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	2.42798	0.015
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	1.20325	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.83582
12-2/M82	N/A	N/A
12-4/M82	1.31113	0.655
1-3/M82	1.02504
2-1-1/M82	1.18165
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	0.95365
4-3/M82	1.46223
5-3/M82	0.7838	0.395
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.31804
7-2/M82	0.9115
9-3-2/M82	1.00209	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.85331	0.277
IL2-6/WTpooled	0.57443	0.473
IL7-5/WTpooled	0.72314	1
IL7-3/WTpooled	2.03418	1
IL12-4/WTpooled	1.09326	0.891
IL1-4/WTpooled	1.51565	0.426
WT/WTpooled	1.0422	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	1.03088	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94135	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.25333	1
DC3000/delta hrp 24h	0.62274	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.98031
DC3000 delta B/DC3000 delta AB	0.8556	0.23

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	1.02873	1
Var 0h	1.05952	0.259
Var 12h I row2-row1	1.09395	0.242
Var 12h NI row2-row1	1.01985	1
Var 36h I row2-row1	0.89874	1
Var 36h NI row2-row1	1.02172	1
Var 60h I row2-row1	1.47888	1
Var 60h NI row2-row1	1.05809	0.904
Time course 0hI-0hNI	1.01027	1
Time course 12hI-12hNI	0.96613	0.698
Time course 36hI-36hNI	0.94441	0.225
Time course 60hI-60hNI	0.79611	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)	1.52606	0.862
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	0.7793	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02319	1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.33286	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	1.26167	0.413