Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.4.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.7758	0.173
27DAP/17DAP	1.05323	0.922
39DAP/27DAP	0.96571	0.7
41DAP/39DAP	1.25512	0.685
42DAP/41DAP	1.16344	0.868
43DAP/42DAP	1.1234	1
47DAP/43DAP	0.97449	0.868
52DAP/47DAP	1.75343	0.228
57DAP/52DAP	0.91071	0.849

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9448	0.284
17DAP/reference	0.97899	0.63
27DAP/reference	1.00034	0.867
39DAP/reference	1.05919	0.104
41DAP/reference	1.00339	1
42DAP/reference	1.15534	0.002
43DAP/reference	1.23393	0.011
47DAP/reference	1.16106	0.024
52DAP/reference	0.96503	0.461
57DAP/reference	0.97604	0.526

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0169	0.99
27DAP/17DAP	0.85447	0.218
39DAP/27DAP	1.12955	0.373
41DAP/39DAP	0.8751	0.093
42DAP/41DAP	1.14154	0.389
43DAP/42DAP	1.94319	0.013
47DAP/43DAP	0.94801	0.554
52DAP/47DAP	0.92022	0.382
57DAP/52DAP	1.06451	0.654
57DAP/7DAP	0.83624	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06542	0.6
17DAP/reference	0.88261	0.049
27DAP/reference	0.84259	0.011
39DAP/reference	0.87379	0.015
41DAP/reference	0.91157	0.03
42DAP/reference	0.92417	0.16
43DAP/reference	1.04131	0.537
47DAP/reference	1.04012	0.854
52DAP/reference	0.89664	0.106
57DAP/reference	0.91617	0.223

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06976	0.47
17DAP/reference	0.9552	0.434
27DAP/reference	0.96965	0.483
39DAP/reference	0.9369	0.281
41DAP/reference	0.92897	0.268
42DAP/reference	0.9357	0.321
43DAP/reference	1.03359	0.854
47DAP/reference	0.99886	0.77
52DAP/reference	0.81657	0.02
57DAP/reference	1.02901	0.754

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04303	0.602
17DAP/reference	0.95586	0.499
27DAP/reference	0.81907	0.043
39DAP/reference	1.07025	0.819
41DAP/reference	0.87881	0.096
42DAP/reference	1.04485	0.671
43DAP/reference	1.04605	0.646
47DAP/reference	1.41284	0.006
52DAP/reference	1.27834	0.335
57DAP/reference	0.94849	0.372

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95807	1
26DAP/20DAP	1.3923	0.24
34DAP/26DAP	0.69847	0.301
51DAP/34DAP	1.02817	0.909
52DAP/51DAP	0.99073	1
53DAP/52DAP	0.98811	0.951
55DAP/53DAP	0.90677	0.282
57DAP/55DAP	1.35379	0.301
62DAP/57DAP	1.12561	0.935
68DAP/62DAP	1.00776	0.914
68DAP/14DAP	1.49221	0.17

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.35098	0.326

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.5787	0.126
Mature Green Tomato/Ripe Tomato	0.45062	0.026
Immature Eggplant/Mature Eggplant	0.62746	0.07
Ripe Pepper/Ripe Tomato	0.82095	0.224
Mature Eggplant/Ripe Tomato	0.30203	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.32951	0.536
1-1-2/M82	1.1041	1
12-2/M82	1.1568	1
12-4/M82	1.05	1
1-3/M82	1.20508	0.479
2-1-1/M82	1.00797	1
2-1/M82	0.63618
2-6/M82	1.29974	0.425
3-2/M82	0.9752	1
4-1-1/M82	1.14968	1
4-1/M82	1.28111	1
4-3-2/M82	1.16851	0.508
4-3/M82	1.61231	0.268
5-3/M82	0.85345	0.642
6-2/M82	0.94151	1
6-3/M82	0.99331	1
7-1/M82	0.85785	0.803
7-2/M82	1.1665	0.385
9-3-2/M82	1.28662	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.61215
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.23246
IL12-4/WTpooled	0.40599	0.581
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	1.20967	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	0.94823	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06596	0.921
DC3000/delta hrp 6h	0.94107	0.95
DC3000/delta hrp 12h	1.1411	1
DC3000/delta hrp 24h	1.15272	0.243

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.74937	0.028
DC3000 delta B/DC3000 delta AB	0.92134	0.497

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.86669	1
Exp 36h	0.7484	0.661
Exp 60h	0.75516	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.10278	0.594
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.97758	0.662
transgenic ySAMdc/azygous control (breaker)	1.40024	0.166
transgenic ySAMdc/azygous control (red)	1.20114	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07144	0.034

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.79859	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.58533	0.083
Manapal/WT (break)	1.4456	0.13
Manapal/WT (red)	1.66994	0.164