Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-3.3.13.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.36915	0.602
27DAP/17DAP	0.96563	0.973
39DAP/27DAP	0.96345	0.594
41DAP/39DAP	1.04516	0.894
42DAP/41DAP	0.97493	1
43DAP/42DAP	1.01865	1
47DAP/43DAP	1.01627	0.999
52DAP/47DAP	1.00341	0.971
57DAP/52DAP	1.03667	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9619	0.476
17DAP/reference	0.93634	0.278
27DAP/reference	0.94471	0.417
39DAP/reference	0.90137	0.118
41DAP/reference	0.90299	0.114
42DAP/reference	1.03052	0.414
43DAP/reference	0.95807	0.631
47DAP/reference	0.96848	0.279
52DAP/reference	0.95805	0.461
57DAP/reference	0.99893	0.736

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0236	0.662
27DAP/17DAP	1.00013	1
39DAP/27DAP	0.99972	1
41DAP/39DAP	1.001	1
42DAP/41DAP	0.999	0.926
43DAP/42DAP	1.04195	0.103
47DAP/43DAP	1.02804	0.827
52DAP/47DAP	0.96156	0.671
57DAP/52DAP	1.00518	1
57DAP/7DAP	0.94925	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94632	0.224
17DAP/reference	0.96785	0.22
27DAP/reference	0.9484	0.017
39DAP/reference	1.04459	0.107
41DAP/reference	1.00601	1
42DAP/reference	1.0299	0.534
43DAP/reference	0.98196	0.48
47DAP/reference	0.97266	0.168
52DAP/reference	1.01951	0.428
57DAP/reference	0.96927	0.314

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93523	0.296
17DAP/reference	0.95846	0.422
27DAP/reference	0.90484	0.181
39DAP/reference	0.94094	0.165
41DAP/reference	0.90256	0.13
42DAP/reference	0.96365	0.392
43DAP/reference	0.88026	0.046
47DAP/reference	1.04463	0.413
52DAP/reference	0.8757	0.051
57DAP/reference	0.94416	0.194

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98201	0.29
17DAP/reference	0.98307	0.55
27DAP/reference	0.99738	0.805
39DAP/reference	0.96136	0.133
41DAP/reference	0.9294	0.07
42DAP/reference	1.02336	0.818
43DAP/reference	1.02669	0.755
47DAP/reference	1.0444	0.704
52DAP/reference	0.98638	0.781
57DAP/reference	1.1586	0.164

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99029	1
26DAP/20DAP	1.05557	0.778
34DAP/26DAP	1.02009	1
51DAP/34DAP	1.00146	1
52DAP/51DAP	0.99618	1
53DAP/52DAP	N/A	N/A
55DAP/53DAP	N/A	N/A
57DAP/55DAP	1.11547	0.881
62DAP/57DAP	0.96252	0.994
68DAP/62DAP	1.45532	0.507
68DAP/14DAP	1.14616	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.03785	0.627

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.51253	0.059
Mature Green Tomato/Ripe Tomato	1.00685	0.715
Immature Eggplant/Mature Eggplant	1.27959	0.215
Ripe Pepper/Ripe Tomato	1.72246	1
Mature Eggplant/Ripe Tomato	1.59285	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96664	0.961
1-1-2/M82	1.01381	1
12-2/M82	0.91691	0.955
12-4/M82	0.99498	1
1-3/M82	0.94018	0.441
2-1-1/M82	0.86629	0.465
2-1/M82	1.49489	1
2-6/M82	0.95038	1
3-2/M82	0.96577	0.752
4-1-1/M82	1.07994	1
4-1/M82	0.91314	0.737
4-3-2/M82	0.85355	1
4-3/M82	0.87385	0.72
5-3/M82	1.00082	1
6-2/M82	0.99771	1
6-3/M82	1.00403	1
7-1/M82	1.02492	1
7-2/M82	0.93651	0.796
9-3-2/M82	0.89222	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.02409	0.493
IL2-6/WTpooled	0.95273	1
IL7-5/WTpooled	0.91633	1
IL7-3/WTpooled	1.20186	1
IL12-4/WTpooled	0.94598	1
IL1-4/WTpooled	1.10101	1
WT/WTpooled	1.00636	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	1.08393	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93542	1
DC3000/delta hrp 6h	0.99584	0.95
DC3000/delta hrp 12h	1.07263	1
DC3000/delta hrp 24h	1.05057	0.62

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.18658	0.068
DC3000 delta B/DC3000 delta AB	1.04706	0.516

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.05361	1
Exp 36h	1.19465	0.693
Exp 60h	1.2487	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04427	1
Var 0h	0.8405	0.332
Var 12h I row2-row1	1.16385	0.224
Var 12h NI row2-row1	0.95979	0.82
Var 36h I row2-row1	1.08378	1
Var 36h NI row2-row1	0.98035	0.852
Var 60h I row2-row1	0.95026	0.285
Var 60h NI row2-row1	1.20811	0.904
Time course 0hI-0hNI	1.05569	0.852
Time course 12hI-12hNI	1.06616	0.58
Time course 36hI-36hNI	1.0951	0.056
Time course 60hI-60hNI	1.16268	0.08

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)	0.8827	0.391
transgenic ySAMdc/azygous control (breaker)	1.33536	1
transgenic ySAMdc/azygous control (red)	1.26939	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98011	0.334

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.38223	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.46966	0.172
Manapal/WT (break)	0.76563	0.333
Manapal/WT (red)	0.6543	0.181