Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.6.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07184	0.964
27DAP/17DAP	0.79161	0.403
39DAP/27DAP	1.0512	0.876
41DAP/39DAP	1.12368	0.708
42DAP/41DAP	1.12114	0.967
43DAP/42DAP	1.11812	0.937
47DAP/43DAP	1.36209	0.618
52DAP/47DAP	1.32259	0.608
57DAP/52DAP	1.69533	0.826

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95986	0.455
17DAP/reference	1.20291	0.017
27DAP/reference	1.00277	0.923
39DAP/reference	1.17827	0.106
41DAP/reference	1.12884	0.171
42DAP/reference	0.95252	0.305
43DAP/reference	1.19611	0.042
47DAP/reference	1.20426	0.125
52DAP/reference	0.96228	0.405
57DAP/reference	0.89919	0.124

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.66602	0.051
27DAP/17DAP	0.96598	0.854
39DAP/27DAP	1.05703	0.659
41DAP/39DAP	0.9557	0.923
42DAP/41DAP	1.3238	0.12
43DAP/42DAP	0.8603	0.181
47DAP/43DAP	1.2011	0.756
52DAP/47DAP	0.95282	0.837
57DAP/52DAP	0.87603	0.411
57DAP/7DAP	1.13145	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77874	0.326
17DAP/reference	0.85243	0.192
27DAP/reference	1.44413	0.041
39DAP/reference	0.89999	0.146
41DAP/reference	1.0681	0.637
42DAP/reference	1.11368	0.686
43DAP/reference	1.10107	0.307
47DAP/reference	1.06949	0.582
52DAP/reference	1.09896	0.599
57DAP/reference	0.95757	0.367

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09712	0.719
17DAP/reference	1.02695	1
27DAP/reference	1.12173	0.203
39DAP/reference	0.99851	0.661
41DAP/reference	1.01312	1
42DAP/reference	1.01084	0.723
43DAP/reference	1.41149	0.111
47DAP/reference	1.14828	0.087
52DAP/reference	0.90114	0.171
57DAP/reference	1.11155	0.409

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94896	0.566
17DAP/reference	1.26555	0.209
27DAP/reference	1.1211	0.487
39DAP/reference	1.29305	0.048
41DAP/reference	1.34429	0.023
42DAP/reference	0.9683	0.671
43DAP/reference	1.16571	0.452
47DAP/reference	0.95346	0.421
52DAP/reference	1.19612	0.457
57DAP/reference	1.08526	0.814

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9995	1
26DAP/20DAP	0.9157	1
34DAP/26DAP	0.83492	0.653
51DAP/34DAP	9.77746	0.022
52DAP/51DAP	0.45105	0.079
53DAP/52DAP	4.65948	0.02
55DAP/53DAP	0.93635	0.686
57DAP/55DAP	0.76929	0.327
62DAP/57DAP	1.38229	0.767
68DAP/62DAP	1.53405	0.21
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.13704	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.91678	0.491
Mature Green Tomato/Ripe Tomato	4.41909
Immature Eggplant/Mature Eggplant	0.80029	0.366
Ripe Pepper/Ripe Tomato	33.2432	1
Mature Eggplant/Ripe Tomato	10.8915	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.84157
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.03751
6-2/M82	N/A	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	1.13968	0.277
IL2-6/WTpooled	1.03916	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.8426	0.294
IL12-4/WTpooled	0.9326	1
IL1-4/WTpooled	1.05261	1
WT/WTpooled	0.94648	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	0.81338	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	0.82616	0.95
DC3000/delta hrp 12h	1.03706	1
DC3000/delta hrp 24h	0.36712	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.43303
DC3000 delta B/DC3000 delta AB	0.47147	0.317

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88373	1
Exp 36h	1.17715	1
Exp 60h	1.2504	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96898	1
Var 0h	0.60187	0.374
Var 12h I row2-row1	1.1015	0.263
Var 12h NI row2-row1	0.85106	0.82
Var 36h I row2-row1	0.94599	1
Var 36h NI row2-row1	1.26858	1
Var 60h I row2-row1	1.14758	0.502
Var 60h NI row2-row1	0.9573	1
Time course 0hI-0hNI	1.18279	0.344
Time course 12hI-12hNI	0.86932	0.259
Time course 36hI-36hNI	0.78328	0.035
Time course 60hI-60hNI	0.60685	0.009

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)	0.9922	0.862
transgenic ySAMdc/azygous control (breaker)	0.51329	0.142
transgenic ySAMdc/azygous control (red)	0.86839	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02215	0.287

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.67856	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.75085	0.172
Manapal/WT (break)	1.13813	1
Manapal/WT (red)	N/A	N/A