Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-2.1.9.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96289	0.728
27DAP/17DAP	0.99597	0.863
39DAP/27DAP	0.85988	0.62
41DAP/39DAP	1.61151	0.553
42DAP/41DAP	1.42814	0.908
43DAP/42DAP	0.90884	0.827
47DAP/43DAP	0.99855	0.804
52DAP/47DAP	1.35533	0.856
57DAP/52DAP	1.36375	0.72

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94751	0.39
17DAP/reference	0.85808	0.043
27DAP/reference	1.06285	0.66
39DAP/reference	1.17913	0.165
41DAP/reference	0.99836	0.814
42DAP/reference	0.84288	0.015
43DAP/reference	1.03302	0.73
47DAP/reference	0.90965	0.077
52DAP/reference	1.22055	0.021
57DAP/reference	1.22221	0.017

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.35432	0.406
27DAP/17DAP	1.08994	0.9
39DAP/27DAP	1.15473	0.596
41DAP/39DAP	0.98748	1
42DAP/41DAP	0.9403	0.584
43DAP/42DAP	1.17713	0.212
47DAP/43DAP	1.04327	0.853
52DAP/47DAP	1.10019	0.816
57DAP/52DAP	1.08713	0.798
57DAP/7DAP	1.82552	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.41473	0.047
17DAP/reference	1.9224	0.006
27DAP/reference	2.02712	0.006
39DAP/reference	2.13546	0.005
41DAP/reference	1.8504	0.008
42DAP/reference	1.69932	0.007
43DAP/reference	1.76082	0.006
47DAP/reference	1.28866	0.353
52DAP/reference	1.45796	0.008
57DAP/reference	1.74896	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28157	0.22
17DAP/reference	0.81875	0.072
27DAP/reference	1.03277	1
39DAP/reference	1.21899	0.036
41DAP/reference	1.26401	0.042
42DAP/reference	0.90333	0.237
43DAP/reference	1.06316	0.997
47DAP/reference	1.03707	0.658
52DAP/reference	1.59798	0.006
57DAP/reference	1.21607	0.031

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30456	0.063
17DAP/reference	0.95985	0.571
27DAP/reference	1.29233	0.067
39DAP/reference	1.15786	0.235
41DAP/reference	1.24237	0.017
42DAP/reference	1.45367	0.046
43DAP/reference	1.39712	0.082
47DAP/reference	0.95089	0.396
52DAP/reference	2.07209	0.082
57DAP/reference	1.56511	0.034

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.92047	0.773
26DAP/20DAP	1.3961	0.477
34DAP/26DAP	0.99995	1
51DAP/34DAP	1.0038	0.957
52DAP/51DAP	1.11193	0.848
53DAP/52DAP	1.15031	0.623
55DAP/53DAP	1.52316	0.118
57DAP/55DAP	14.1642	0.745
62DAP/57DAP	0.60406	0.681
68DAP/62DAP	1.59376	0.034
68DAP/14DAP	3.24908	0.02

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.78939	0.285

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.7565	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.01717	1
Mature Eggplant/Ripe Tomato	0.16657	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.31773	N/A
1-1-2/M82	0.99455	N/A
12-2/M82	N/A	N/A
12-4/M82	1.03869	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.59942	N/A
3-2/M82	0.78871	N/A
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	0.86943	0.642
6-2/M82	0.92279	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.92428	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.95521	N/A
WT/WTpooled	1.13883	N/A

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	0.99575	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98348	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.05458	1
DC3000/delta hrp 24h	0.95222	0.692

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.96846	0.691
DC3000 delta B/DC3000 delta AB	1.36338	0.386

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93666	0.203
Exp 36h	1.01332	0.326
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	N/A	N/A
Var 0h	1.04062	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	1.10159	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	1.10069	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	1.10358	0.361
Time course 0hI-0hNI	0.90101	0.397
Time course 12hI-12hNI	1.01155	1
Time course 36hI-36hNI	1.11069	0.513
Time course 60hI-60hNI	1.03253	0.673

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)	1.05356	0.397
transgenic ySAMdc/azygous control (breaker)	0.82765	0.173
transgenic ySAMdc/azygous control (red)	1.00956	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00413	0.811

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.91401	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.91166	1
Manapal/WT (break)	1.16556	1
Manapal/WT (red)	1.22464	0.413