Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.2.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85909	0.249
27DAP/17DAP	0.74942	0.207
39DAP/27DAP	0.83921	0.268
41DAP/39DAP	1.31192	0.387
42DAP/41DAP	1.30123	0.514
43DAP/42DAP	1.02535	0.937
47DAP/43DAP	0.85555	0.55
52DAP/47DAP	1.01603	1
57DAP/52DAP	0.89985	0.852

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05688	0.278
17DAP/reference	1.01554	0.442
27DAP/reference	0.98287	0.525
39DAP/reference	0.91056	0.053
41DAP/reference	0.9336	0.085
42DAP/reference	0.9169	0.029
43DAP/reference	0.94823	0.48
47DAP/reference	0.9178	0.019
52DAP/reference	0.90292	0.195
57DAP/reference	0.70697	0.042

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06117	1
27DAP/17DAP	0.97777	0.887
39DAP/27DAP	0.99548	1
41DAP/39DAP	1.2042	0.579
42DAP/41DAP	1.08119	0.593
43DAP/42DAP	1.04616	0.699
47DAP/43DAP	1.05361	0.833
52DAP/47DAP	1.08949	0.73
57DAP/52DAP	1.06646	0.753
57DAP/7DAP	1.20734	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19874	0.235
17DAP/reference	0.85489	0.253
27DAP/reference	0.93862	0.402
39DAP/reference	0.97177	0.552
41DAP/reference	1.06321	0.701
42DAP/reference	1.00909	0.554
43DAP/reference	0.80886	0.1
47DAP/reference	0.96323	0.504
52DAP/reference	0.94325	0.304
57DAP/reference	1.00745	0.629

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11813	0.104
17DAP/reference	1.01585	0.924
27DAP/reference	0.86329	0.115
39DAP/reference	0.80732	0.016
41DAP/reference	0.83957	0.036
42DAP/reference	0.84564	0.021
43DAP/reference	0.83348	0.068
47DAP/reference	0.87234	0.023
52DAP/reference	0.85292	0.005
57DAP/reference	0.85125	0.079

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82321	0.092
17DAP/reference	0.99673	0.81
27DAP/reference	0.87281	0.067
39DAP/reference	0.9871	0.755
41DAP/reference	1.07256	1
42DAP/reference	0.85319	0.287
43DAP/reference	0.93682	0.449
47DAP/reference	0.92948	0.132
52DAP/reference	0.8376	0.197
57DAP/reference	0.7319	0.051

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9717	1
26DAP/20DAP	0.8494	0.512
34DAP/26DAP	0.80462	0.462
51DAP/34DAP	1.15916	0.483
52DAP/51DAP	0.88134	1
53DAP/52DAP	1.02808	0.921
55DAP/53DAP	1.10666	0.719
57DAP/55DAP	0.82435	0.344
62DAP/57DAP	1.16231	0.515
68DAP/62DAP	1.06894	0.95
68DAP/14DAP	0.97316	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.92266	0.322

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.77794	0.058
Mature Green Tomato/Ripe Tomato	1.77623	0.015
Immature Eggplant/Mature Eggplant	0.3517	0.057
Ripe Pepper/Ripe Tomato	2.47458	1
Mature Eggplant/Ripe Tomato	12.5464	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04548	0.742
1-1-2/M82	0.91497
12-2/M82	N/A	N/A
12-4/M82	1.11579	1
1-3/M82	0.88632	0.501
2-1-1/M82	1.2194
2-1/M82	N/A	N/A
2-6/M82	1.02997	0.329
3-2/M82	1.01483
4-1-1/M82	0.8219	1
4-1/M82	0.92493	1
4-3-2/M82	0.99051	1
4-3/M82	0.92435	1
5-3/M82	0.95267	0.642
6-2/M82	0.97446	1
6-3/M82	0.76787
7-1/M82	N/A	N/A
7-2/M82	1.05457	1
9-3-2/M82	0.95615	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.8185	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.94317	1
IL12-4/WTpooled	0.92264	1
IL1-4/WTpooled	1.02391
WT/WTpooled	1.03745	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	0.77459	0.216

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95007	1
DC3000/delta hrp 6h	0.86735	0.95
DC3000/delta hrp 12h	0.92732	1
DC3000/delta hrp 24h	0.83873	0.079

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.49135	0.024
DC3000 delta B/DC3000 delta AB	0.56272	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97346	1
Exp 36h	0.80184	0.623
Exp 60h	0.63937	0.253

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96321	1
Var 0h	0.8633	0.457
Var 12h I row2-row1	0.99983	1
Var 12h NI row2-row1	1.0112	1
Var 36h I row2-row1	1.05076	1
Var 36h NI row2-row1	1.13374	1
Var 60h I row2-row1	1.07204	0.562
Var 60h NI row2-row1	1.13722	0.4
Time course 0hI-0hNI	1.02137	0.799
Time course 12hI-12hNI	0.91011	0.115
Time course 36hI-36hNI	0.77492	0.023
Time course 60hI-60hNI	0.48676	0.006

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)	1.02288	0.798
transgenic ySAMdc/azygous control (breaker)	1.09584	0.248
transgenic ySAMdc/azygous control (red)	1.05619	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97225	0.471

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.309	0.228

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.95616	0.084
Manapal/WT (break)	5.27993	0.123
Manapal/WT (red)	2.80489	0.222