Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.6.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.2428	0.588
27DAP/17DAP	0.85868	0.622
39DAP/27DAP	1.38956	0.864
41DAP/39DAP	1.02584	1
42DAP/41DAP	0.92135	1
43DAP/42DAP	1.10768	1
47DAP/43DAP	1.13294	0.429
52DAP/47DAP	0.86191	0.657
57DAP/52DAP	1.16441	0.958

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0288	0.788
17DAP/reference	1.12338	0.053
27DAP/reference	1.02703	0.831
39DAP/reference	1.07525	0.497
41DAP/reference	1.0833	0.171
42DAP/reference	0.86611	0.01
43DAP/reference	0.9584	0.394
47DAP/reference	0.98493	0.503
52DAP/reference	0.99721	0.689
57DAP/reference	0.89589	0.056

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13581	0.858
27DAP/17DAP	1.20034	0.353
39DAP/27DAP	1.00852	1
41DAP/39DAP	0.9579	0.861
42DAP/41DAP	0.9352	0.548
43DAP/42DAP	0.93909	0.709
47DAP/43DAP	1.08598	0.735
52DAP/47DAP	1.05334	0.819
57DAP/52DAP	0.81975	0.161
57DAP/7DAP	0.84977

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11645	0.332
17DAP/reference	1.42382	0.269
27DAP/reference	1.12092	0.197
39DAP/reference	1.2845	0.015
41DAP/reference	1.02317	1
42DAP/reference	1.34295	0.024
43DAP/reference	1.05843	0.483
47DAP/reference	1.30334	0.395
52DAP/reference	1.28112	0.066
57DAP/reference	1.23203	0.076

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9805	0.77
17DAP/reference	1.07325	0.385
27DAP/reference	0.98558	0.619
39DAP/reference	1.02156	1
41DAP/reference	0.83725	0.121
42DAP/reference	0.78002	0.018
43DAP/reference	1.00509	0.774
47DAP/reference	0.97352	0.434
52DAP/reference	1.06455	0.838
57DAP/reference	1.11284	0.409

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18448	0.19
17DAP/reference	0.95231	0.592
27DAP/reference	1.35713	0.467
39DAP/reference	1.01308	1
41DAP/reference	1.19784	0.357
42DAP/reference	1.15868	0.612
43DAP/reference	1.04395	0.894
47DAP/reference	0.97536	0.478
52DAP/reference	1.1955	0.247
57DAP/reference	0.95534	0.468

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03122	0.966
26DAP/20DAP	0.97307	1
34DAP/26DAP	1.22215	0.819
51DAP/34DAP	1.36645	0.058
52DAP/51DAP	1.1604	0.534
53DAP/52DAP	0.79651	0.371
55DAP/53DAP	0.96188	0.852
57DAP/55DAP	0.95839	0.859
62DAP/57DAP	0.79864	0.28
68DAP/62DAP	0.94249	0.834
68DAP/14DAP	1.13119	0.091

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.14084	0.954

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.83067	0.418
Mature Green Tomato/Ripe Tomato	1.05017	0.948
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.86096	1
Mature Eggplant/Ripe Tomato	2.02241	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.95256	1
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	0.88904
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.28993
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.97354	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.13672	1
7-2/M82	0.93336
9-3-2/M82	1.19971	0.125

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	2.14682
IL2-6/WTpooled	1.1412	0.419
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.13844	0.362
IL12-4/WTpooled	0.7585	0.566
IL1-4/WTpooled	1.07814	0.421
WT/WTpooled	0.81031	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	1.01001	1

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	1.17722	0.857
DC3000/delta hrp 12h	1.08471	1
DC3000/delta hrp 24h	1.07204	0.383

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	0.90668	1
Exp 36h	1.02406	0.489
Exp 60h	0.91805	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99434	1
Var 0h	0.50224	1
Var 12h I row2-row1	1.59745	0.443
Var 12h NI row2-row1	1.15324	1
Var 36h I row2-row1	0.81001	1
Var 36h NI row2-row1	1.10765	1
Var 60h I row2-row1	0.89281	0.306
Var 60h NI row2-row1	0.91034	0.977
Time course 0hI-0hNI	1.03335	0.799
Time course 12hI-12hNI	1.05285	0.756
Time course 36hI-36hNI	1.08461	0.128
Time course 60hI-60hNI	0.94781	0.047

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)	0.91703	0.338
transgenic ySAMdc/azygous control (breaker)	0.78793	0.173
transgenic ySAMdc/azygous control (red)	1.07387	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08116	0.08

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.8553	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.98183	1
Manapal/WT (break)	1.15244	0.381
Manapal/WT (red)	0.81926	0.229