Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.14.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.31252	0.381
27DAP/17DAP	1.11316	0.854
39DAP/27DAP	0.70517	0.304
41DAP/39DAP	0.78308	0.367
42DAP/41DAP	1.04283	1
43DAP/42DAP	0.9205	0.867
47DAP/43DAP	1.07466	0.842
52DAP/47DAP	0.81433	0.54
57DAP/52DAP	0.98548	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07897	0.278
17DAP/reference	1.06487	0.154
27DAP/reference	0.97069	0.61
39DAP/reference	0.95795	0.446
41DAP/reference	0.91736	0.039
42DAP/reference	0.89769	0.025
43DAP/reference	0.91187	0.093
47DAP/reference	0.91242	0.038
52DAP/reference	0.98144	0.53
57DAP/reference	1.03357	0.829

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.39076	0.057
27DAP/17DAP	0.80175	0.339
39DAP/27DAP	0.76956	0.072
41DAP/39DAP	1.03824	0.887
42DAP/41DAP	0.96859	0.721
43DAP/42DAP	0.72317	0.022
47DAP/43DAP	0.92089	0.543
52DAP/47DAP	0.91649	0.746
57DAP/52DAP	1.36306	0.393
57DAP/7DAP	0.83339	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0696	0.435
17DAP/reference	1.5027	0.006
27DAP/reference	1.61652	0.008
39DAP/reference	1.95349	0.006
41DAP/reference	1.64641	0.011
42DAP/reference	1.83576	0.007
43DAP/reference	1.69273	0.008
47DAP/reference	1.29835	0.272
52DAP/reference	1.96892	0.02
57DAP/reference	1.36997	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05806	0.491
17DAP/reference	1.19147	0.101
27DAP/reference	0.96233	0.452
39DAP/reference	1.04993	0.529
41DAP/reference	1.01142	1
42DAP/reference	1.00206	0.723
43DAP/reference	1.00918	0.814
47DAP/reference	0.98833	0.5
52DAP/reference	0.98797	0.576
57DAP/reference	1.01164	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20532	0.06
17DAP/reference	1.12741	0.194
27DAP/reference	1.33955	0.061
39DAP/reference	1.29011	0.072
41DAP/reference	1.31835	0.017
42DAP/reference	1.45346	0.009
43DAP/reference	1.37517	0.076
47DAP/reference	0.93162	0.207
52DAP/reference	1.33861	0.153
57DAP/reference	1.17416	0.316

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91903	1
26DAP/20DAP	1.20547	0.427
34DAP/26DAP	0.8807	0.462
51DAP/34DAP	1.19761	0.241
52DAP/51DAP	0.83669	0.151
53DAP/52DAP	0.9394	0.783
55DAP/53DAP	1.46474	0.927
57DAP/55DAP	1.047	0.898
62DAP/57DAP	0.99895	0.994
68DAP/62DAP	1.24726	0.792
68DAP/14DAP	1.00455	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.92877	0.097

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.98706	0.058
Mature Green Tomato/Ripe Tomato	5.46155	0.015
Immature Eggplant/Mature Eggplant	1.13143	0.248
Ripe Pepper/Ripe Tomato	1.9296	0.258
Mature Eggplant/Ripe Tomato	1.67209	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.99816
12-2/M82	1.18486
12-4/M82	0.79921
1-3/M82	N/A	N/A
2-1-1/M82	0.82529
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.87683
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	0.87243	0.642
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.18045
7-2/M82	0.98314
9-3-2/M82	1.13591

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.9142
IL2-6/WTpooled	0.87287	0.473
IL7-5/WTpooled	0.5909
IL7-3/WTpooled	0.98654	1
IL12-4/WTpooled	1.01681	0.839
IL1-4/WTpooled	1.04036	1
WT/WTpooled	0.98062	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	1.00189	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97504	1
DC3000/delta hrp 6h	1.00999	1
DC3000/delta hrp 12h	0.97808	1
DC3000/delta hrp 24h	1.15999	0.347

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.08762	1
Exp 36h	0.92118	0.749
Exp 60h	0.9323	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9837
Var 0h	0.40828	1
Var 12h I row2-row1	0.91825	0.514
Var 12h NI row2-row1	1.09329	0.281
Var 36h I row2-row1	1.11396	1
Var 36h NI row2-row1	0.60206	0.743
Var 60h I row2-row1	1.09398	0.562
Var 60h NI row2-row1	0.8222	0.866
Time course 0hI-0hNI	1.11456	0.451
Time course 12hI-12hNI	0.95488	0.698
Time course 36hI-36hNI	1.06581	0.316
Time course 60hI-60hNI	0.80139	0.047

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)	1.17614	0.268
transgenic ySAMdc/azygous control (breaker)	0.77041	0.137
transgenic ySAMdc/azygous control (red)	1.05545	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.12788	0.061

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.59444	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.55718	0.172
Manapal/WT (break)	1.08966	1
Manapal/WT (red)	0.88449	0.424