Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.10.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17565	0.911
27DAP/17DAP	1.87645	0.435
39DAP/27DAP	2.16385	0.111
41DAP/39DAP	0.84634	0.407
42DAP/41DAP	2.08736	0.029
43DAP/42DAP	0.75824	0.705
47DAP/43DAP	1.25885	0.542
52DAP/47DAP	0.84498	0.589
57DAP/52DAP	1.20261	0.972

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.6733	0.035
17DAP/reference	0.89937	0.147
27DAP/reference	1.01755	0.934
39DAP/reference	0.98392	0.75
41DAP/reference	1.02535	0.451
42DAP/reference	0.8538	0.012
43DAP/reference	1.15774	0.019
47DAP/reference	0.95811	0.279
52DAP/reference	0.8258	0.053
57DAP/reference	0.99933	0.639

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.789	0.278
27DAP/17DAP	1.09437	0.912
39DAP/27DAP	1.23721	0.227
41DAP/39DAP	1.39478	0.362
42DAP/41DAP	0.92089	0.612
43DAP/42DAP	0.89367	0.101
47DAP/43DAP	1.0863	0.812
52DAP/47DAP	0.77748	0.261
57DAP/52DAP	1.10699	0.858
57DAP/7DAP	1.58922	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11368	0.83
17DAP/reference	1.32326	0.134
27DAP/reference	1.34333	0.16
39DAP/reference	1.2352	0.511
41DAP/reference	1.2458	0.215
42DAP/reference	1.3068	0.308
43DAP/reference	1.15104	0.273
47DAP/reference	1.06208	0.996
52DAP/reference	0.99564	0.679
57DAP/reference	1.1482	0.057

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03005	0.97
17DAP/reference	1.01276	0.673
27DAP/reference	0.97915	0.537
39DAP/reference	1.02369	1
41DAP/reference	1.00302	0.493
42DAP/reference	0.83707	0.15
43DAP/reference	1.86647	0.105
47DAP/reference	2.70079	0.043
52DAP/reference	0.97568	0.469
57DAP/reference	2.21242	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94747	0.455
17DAP/reference	1.03683	0.918
27DAP/reference	1.23758	0.143
39DAP/reference	1.24715	0.1
41DAP/reference	0.88623	0.293
42DAP/reference	1.07294	0.802
43DAP/reference	0.97918	0.639
47DAP/reference	1.01935	0.731
52DAP/reference	1.2521	0.126
57DAP/reference	1.25708	0.604

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01095	1
26DAP/20DAP	1.42028	0.232
34DAP/26DAP	0.81406	0.834
51DAP/34DAP	0.90283	0.555
52DAP/51DAP	0.94445	1
53DAP/52DAP	1.32223	0.678
55DAP/53DAP	1.80931	0.566
57DAP/55DAP	1.22026	1
62DAP/57DAP	1.02119	0.868
68DAP/62DAP	1.3578	0.897
68DAP/14DAP	1.02613

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.53434	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.30035	0.021
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.90503
Mature Eggplant/Ripe Tomato	0.93371

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.60579
1-1-2/M82	0.82064	1
12-2/M82	N/A	N/A
12-4/M82	0.91061
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	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.39388	0.241
4-3/M82	N/A	N/A
5-3/M82	3.45625	0.496
6-2/M82	4.52216	0.253
6-3/M82	1.68527	1
7-1/M82	2.54889
7-2/M82	1.25671
9-3-2/M82	1.40255	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.02941	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.02618	1
IL12-4/WTpooled	0.87784	0.581
IL1-4/WTpooled	0.97092
WT/WTpooled	0.99486	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	1.67613	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.90173	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.27221	1
DC3000/delta hrp 24h	0.72641	0.079

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	66.1097	0.693
Exp 60h	3.05084	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94439
Var 0h	1.09859	0.374
Var 12h I row2-row1	0.86462	0.338
Var 12h NI row2-row1	2.62679	0.649
Var 36h I row2-row1	1.50922	0.41
Var 36h NI row2-row1	0.51442	0.478
Var 60h I row2-row1	0.62521	0.285
Var 60h NI row2-row1	0.68344	0.318
Time course 0hI-0hNI	0.94472	0.751
Time course 12hI-12hNI	1.65703	0.015
Time course 36hI-36hNI	8.69835	0.004
Time course 60hI-60hNI	76.7438	0.008

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	1.81608	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.81042	0.092

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.25355	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.65852	0.105
Manapal/WT (break)	1.09729	1
Manapal/WT (red)	0.81194	0.503