Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.1.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07059	0.863
27DAP/17DAP	0.56603	0.027
39DAP/27DAP	0.71527	0.353
41DAP/39DAP	0.86752	0.475
42DAP/41DAP	0.96104	1
43DAP/42DAP	1.18463	1
47DAP/43DAP	0.82573	0.439
52DAP/47DAP	0.96211	0.823
57DAP/52DAP	0.97853	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02675	0.76
17DAP/reference	1.08406	0.053
27DAP/reference	0.87599	0.073
39DAP/reference	0.97651	0.68
41DAP/reference	0.87059	0.201
42DAP/reference	0.85245	0.005
43DAP/reference	1.08574	0.233
47DAP/reference	0.82062	0.013
52DAP/reference	0.77913	0.147
57DAP/reference	0.82365	0.165

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85071	0.299
27DAP/17DAP	1.07443	0.945
39DAP/27DAP	0.50507	0.032
41DAP/39DAP	0.49942	0.013
42DAP/41DAP	0.99716	0.845
43DAP/42DAP	1.02717	0.699
47DAP/43DAP	0.81277	0.031
52DAP/47DAP	1.01454	0.97
57DAP/52DAP	0.8592	0.454
57DAP/7DAP	0.64987

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.73944	0.027
17DAP/reference	1.34526	0.008
27DAP/reference	1.12995	0.041
39DAP/reference	1.18311	0.411
41DAP/reference	1.10559	0.491
42DAP/reference	1.18728	0.308
43DAP/reference	0.89342	0.04
47DAP/reference	0.72879	0.101
52DAP/reference	1.18135	0.034
57DAP/reference	1.13697	0.057

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89188	0.182
17DAP/reference	0.90829	0.159
27DAP/reference	0.91113	0.327
39DAP/reference	0.77096	0.013
41DAP/reference	0.85838	0.083
42DAP/reference	0.78147	0.024
43DAP/reference	0.75326	0.021
47DAP/reference	0.84579	0.018
52DAP/reference	0.74888	0.004
57DAP/reference	0.68655	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.69006	0.025
17DAP/reference	1.51004	0.146
27DAP/reference	0.93701	0.27
39DAP/reference	1.12224	0.264
41DAP/reference	1.28411	0.009
42DAP/reference	0.86336	0.172
43DAP/reference	0.80774	0.095
47DAP/reference	0.79859	0.027
52DAP/reference	0.78136	0.098
57DAP/reference	0.92636	0.333

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0418	0.966
26DAP/20DAP	0.84376	1
34DAP/26DAP	0.99452	0.97
51DAP/34DAP	0.65089	0.061
52DAP/51DAP	0.96881	1
53DAP/52DAP	0.93212	0.767
55DAP/53DAP	1.06568	0.994
57DAP/55DAP	1.03049	0.899
62DAP/57DAP	1.2458	0.622
68DAP/62DAP	1.07981	0.907
68DAP/14DAP	1.11473	0.694

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.47898	0.028

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.70191	0.058
Mature Green Tomato/Ripe Tomato	3.68756	0.034
Immature Eggplant/Mature Eggplant	0.48293	0.061
Ripe Pepper/Ripe Tomato	1.13331	1
Mature Eggplant/Ripe Tomato	2.7482	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9317	0.944
1-1-2/M82	0.97594	1
12-2/M82	0.97127	0.955
12-4/M82	1.01122	1
1-3/M82	0.65606	0.378
2-1-1/M82	1.21904	0.689
2-1/M82	N/A	N/A
2-6/M82	1.33897	0.505
3-2/M82	0.98663	1
4-1-1/M82	1.1046	1
4-1/M82	0.85093	1
4-3-2/M82	1.03437	1
4-3/M82	0.87676	0.466
5-3/M82	1.0072	1
6-2/M82	1.02254	1
6-3/M82	1.09012	1
7-1/M82	1.15037	0.992
7-2/M82	1.13355	0.385
9-3-2/M82	0.79066	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.19252	0.277
IL2-6/WTpooled	0.91187	1
IL7-5/WTpooled	0.85579	1
IL7-3/WTpooled	0.9802	1
IL12-4/WTpooled	0.75538	0.497
IL1-4/WTpooled	0.93391	0.562
WT/WTpooled	1.01847	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	0.93359	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99133	1
DC3000/delta hrp 6h	0.90241	0.95
DC3000/delta hrp 12h	0.97058	1
DC3000/delta hrp 24h	0.89859	0.163

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.4989	0.024
DC3000 delta B/DC3000 delta AB	0.43776	0.023

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95129	1
Exp 36h	0.85617	0.589
Exp 60h	0.81631	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99647	1
Var 0h	1.05038	0.98
Var 12h I row2-row1	0.74052	0.338
Var 12h NI row2-row1	0.9665	0.906
Var 36h I row2-row1	1.02494	1
Var 36h NI row2-row1	1.19093	1
Var 60h I row2-row1	1.12959	0.562
Var 60h NI row2-row1	1.06031	1
Time course 0hI-0hNI	2.51309	0.799
Time course 12hI-12hNI	0.93898	0.612
Time course 36hI-36hNI	0.78405	0.038
Time course 60hI-60hNI	0.098	0.005

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)	1.13386	0.748
transgenic ySAMdc/azygous control (breaker)	4.1942	0.162
transgenic ySAMdc/azygous control (red)	0.934	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.8472	0.131

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.65011	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.54452	0.083
Manapal/WT (break)	6.86887	0.14
Manapal/WT (red)	5.03956	0.142