Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.15.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92871	0.596
27DAP/17DAP	1.20494	0.833
39DAP/27DAP	0.97731	0.733
41DAP/39DAP	0.92233	0.675
42DAP/41DAP	0.94213	1
43DAP/42DAP	1.0375	1
47DAP/43DAP	1.13904	0.689
52DAP/47DAP	0.80071	0.499
57DAP/52DAP	0.96256	0.947

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91561	0.154
17DAP/reference	1.00763	1
27DAP/reference	1.03153	0.696
39DAP/reference	1.04307	0.474
41DAP/reference	1.05175	0.808
42DAP/reference	0.95082	0.157
43DAP/reference	0.93408	0.41
47DAP/reference	1.00885	1
52DAP/reference	0.95328	0.405
57DAP/reference	1.01175	0.845

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94387	0.526
27DAP/17DAP	1.06106	0.822
39DAP/27DAP	0.93056	0.382
41DAP/39DAP	1.01232	1
42DAP/41DAP	0.94236	0.595
43DAP/42DAP	1.05632	0.103
47DAP/43DAP	1.01736	0.92
52DAP/47DAP	0.99334	0.962
57DAP/52DAP	0.93733	0.531
57DAP/7DAP	0.93852	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03763	0.705
17DAP/reference	1.26834	0.008
27DAP/reference	1.11674	0.017
39DAP/reference	1.09102	0.21
41DAP/reference	1.20842	0.018
42DAP/reference	1.29903	0.021
43DAP/reference	1.69901	0.007
47DAP/reference	1.1229	0.493
52DAP/reference	1.11262	0.197
57DAP/reference	1.66954	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97599	0.592
17DAP/reference	0.92458	0.129
27DAP/reference	0.83749	0.093
39DAP/reference	0.78376	0.083
41DAP/reference	0.97466	0.459
42DAP/reference	0.94334	0.355
43DAP/reference	0.94301	0.404
47DAP/reference	0.9945	0.66
52DAP/reference	0.88109	0.005
57DAP/reference	0.88363	0.024

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9886	0.607
17DAP/reference	1.02634	0.804
27DAP/reference	1.2428	0.023
39DAP/reference	1.14769	0.021
41DAP/reference	1.08812	0.333
42DAP/reference	1.04608	0.789
43DAP/reference	0.94407	0.449
47DAP/reference	0.9442	0.286
52DAP/reference	1.04315	0.952
57DAP/reference	0.86093	0.187

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01239	0.966
26DAP/20DAP	1.02132	1
34DAP/26DAP	0.97217	0.936
51DAP/34DAP	1.1056	0.387
52DAP/51DAP	0.96029	1
53DAP/52DAP	0.88393	0.505
55DAP/53DAP	0.93434	0.761
57DAP/55DAP	1.2227	0.376
62DAP/57DAP	1.0514	1
68DAP/62DAP	0.93921	0.769
68DAP/14DAP	0.73535	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.08675	0.591

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.08497	0.176
Mature Green Tomato/Ripe Tomato	1.25381	0.106
Immature Eggplant/Mature Eggplant	1.41255	0.05
Ripe Pepper/Ripe Tomato	1.10145	1
Mature Eggplant/Ripe Tomato	1.25936	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98224	0.944
1-1-2/M82	0.8551	1
12-2/M82	0.97915	0.727
12-4/M82	0.96443	0.619
1-3/M82	0.98483	1
2-1-1/M82	0.92464	0.683
2-1/M82	1.19483	1
2-6/M82	0.98853	1
3-2/M82	0.99724	1
4-1-1/M82	1.02907	1
4-1/M82	0.80993	1
4-3-2/M82	0.87174	0.698
4-3/M82	0.97396	1
5-3/M82	1.0234	1
6-2/M82	0.9575	0.497
6-3/M82	1.00305	1
7-1/M82	0.9848	1
7-2/M82	0.99201	1
9-3-2/M82	0.94269	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.66107	0.321
IL2-6/WTpooled	2.17498	0.419
IL7-5/WTpooled	1.44971	1
IL7-3/WTpooled	0.50256	0.294
IL12-4/WTpooled	1.65158	0.785
IL1-4/WTpooled	1.21077	0.426
WT/WTpooled	1.07588	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	1.11504

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98672	1
DC3000/delta hrp 6h	0.9353	0.95
DC3000/delta hrp 12h	1.12508	1
DC3000/delta hrp 24h	1.09131	0.347

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.16098	0.042
DC3000 delta B/DC3000 delta AB	1.13213	0.274

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02979	1
Exp 36h	0.8989	0.879
Exp 60h	1.31593	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99204	1
Var 0h	3.76878	0.98
Var 12h I row2-row1	1.18128	0.272
Var 12h NI row2-row1	0.86989	0.494
Var 36h I row2-row1	0.97849	1
Var 36h NI row2-row1	1.19446	0.482
Var 60h I row2-row1	1.24217	0.562
Var 60h NI row2-row1	1.18972	0.904
Time course 0hI-0hNI	1.0206	1
Time course 12hI-12hNI	1.01007	0.867
Time course 36hI-36hNI	0.89146	0.211
Time course 60hI-60hNI	1.02294	1

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)	1.08173	0.408
transgenic ySAMdc/azygous control (breaker)	0.89418	0.49
transgenic ySAMdc/azygous control (red)	0.97165	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93313	0.046

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.90773	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.82333	1
Manapal/WT (break)	0.76135	0.333
Manapal/WT (red)	0.69408	0.181