Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.14.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.78001	0.123
27DAP/17DAP	1.18751	0.798
39DAP/27DAP	1.84474	0.064
41DAP/39DAP	1.47407	0.268
42DAP/41DAP	0.90553	1
43DAP/42DAP	1.18985	0.655
47DAP/43DAP	1.99298	0.239
52DAP/47DAP	1.3911	0.57
57DAP/52DAP	0.89479	0.919

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87954	0.177
17DAP/reference	0.86248	0.069
27DAP/reference	1.15765	0.435
39DAP/reference	0.80641	0.074
41DAP/reference	0.86725	0.201
42DAP/reference	0.81363	0.001
43DAP/reference	0.96807	0.594
47DAP/reference	0.89315	0.055
52DAP/reference	1.01746	1
57DAP/reference	1.16957	0.017

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91573	0.47
27DAP/17DAP	1.15997	0.564
39DAP/27DAP	0.91137	0.477
41DAP/39DAP	0.93999	0.875
42DAP/41DAP	1.23699	0.622
43DAP/42DAP	1.14663	0.324
47DAP/43DAP	0.867	0.387
52DAP/47DAP	0.99332	0.962
57DAP/52DAP	1.37457	0.133
57DAP/7DAP	2.67278	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.33009	0.066
17DAP/reference	1.37421	0.077
27DAP/reference	1.21452	0.107
39DAP/reference	1.16745	0.096
41DAP/reference	1.19543	0.109
42DAP/reference	1.20098	0.174
43DAP/reference	1.19396	0.048
47DAP/reference	0.97613	0.383
52DAP/reference	1.22248	0.076
57DAP/reference	1.11853	0.198

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89239	0.296
17DAP/reference	0.95193	0.41
27DAP/reference	0.89064	0.047
39DAP/reference	0.88099	0.032
41DAP/reference	0.88887	0.115
42DAP/reference	0.78961	0.012
43DAP/reference	0.99592	0.67
47DAP/reference	0.78248	0.017
52DAP/reference	0.86132	0.023
57DAP/reference	0.7599	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18065	0.072
17DAP/reference	1.00899	0.825
27DAP/reference	1.38299	0.03
39DAP/reference	1.1116	0.406
41DAP/reference	1.21833	0.08
42DAP/reference	1.10212	0.529
43DAP/reference	1.12242	0.336
47DAP/reference	0.87522	0.015
52DAP/reference	1.2878	0.312
57DAP/reference	1.06276	0.814

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.30782	0.56
26DAP/20DAP	1.23659	1
34DAP/26DAP	1.41246	1
51DAP/34DAP	1.20367	0.581
52DAP/51DAP	0.87909	1
53DAP/52DAP	1.14619	0.83
55DAP/53DAP	0.72001	0.282
57DAP/55DAP	1.09396	0.826
62DAP/57DAP	0.93772	0.994
68DAP/62DAP	0.76898	0.406
68DAP/14DAP	1.26486	0.328

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.68499	0.057

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.06543	0.417
Mature Green Tomato/Ripe Tomato	0.19489	0.017
Immature Eggplant/Mature Eggplant	0.97626	0.912
Ripe Pepper/Ripe Tomato	1.09117	1
Mature Eggplant/Ripe Tomato	1.29844	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03965	0.742
1-1-2/M82	0.9968	1
12-2/M82	0.8183
12-4/M82	1.15865	1
1-3/M82	0.88383
2-1-1/M82	0.95932
2-1/M82	0.98965	1
2-6/M82	0.86839	1
3-2/M82	0.66752	1
4-1-1/M82	1.33273
4-1/M82	0.87659	0.525
4-3-2/M82	1.20375
4-3/M82	1.33565	1
5-3/M82	0.85354	0.387
6-2/M82	0.96484
6-3/M82	1.0444	1
7-1/M82	1.04012	1
7-2/M82	1.00448
9-3-2/M82	1.28138	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.68872
IL2-6/WTpooled	1.93211	0.395
IL7-5/WTpooled	0.64163
IL7-3/WTpooled	0.77576	0.25
IL12-4/WTpooled	0.92826	0.71
IL1-4/WTpooled	1.97173	0.426
WT/WTpooled	0.87441	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	1.07327	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97821	1
DC3000/delta hrp 6h	0.88336	0.95
DC3000/delta hrp 12h	0.95678	1
DC3000/delta hrp 24h	1.14338	0.322

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	0.95318	1
Exp 36h	1.00144	1
Exp 60h	0.88401	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98928	1
Var 0h	0.93521	0.933
Var 12h I row2-row1	1.03082	1
Var 12h NI row2-row1	1.09085	1
Var 36h I row2-row1	1.09481	0.908
Var 36h NI row2-row1	0.69132	0.61
Var 60h I row2-row1	0.93191	0.285
Var 60h NI row2-row1	1.02413	1
Time course 0hI-0hNI	0.93582	0.687
Time course 12hI-12hNI	0.9658	0.739
Time course 36hI-36hNI	1.0377	0.722
Time course 60hI-60hNI	1.46834	0.01

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)	0.89268	0.315
transgenic ySAMdc/azygous control (breaker)	1.09524	0.248
transgenic ySAMdc/azygous control (red)	1.00689	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00272	0.958

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.85736	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.85295	1
Manapal/WT (break)	0.70024	0.333
Manapal/WT (red)	0.83516	0.229