Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.17.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.39475	0.443
27DAP/17DAP	0.72822	0.273
39DAP/27DAP	1.45686	0.344
41DAP/39DAP	2.25581	0.223
42DAP/41DAP	1.25146	0.777
43DAP/42DAP	1.82269	0.207
47DAP/43DAP	1.98077	0.223
52DAP/47DAP	1.7209	0.266
57DAP/52DAP	1.04368	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05216	1
17DAP/reference	1.49967	0.04
27DAP/reference	1.21987	0.264
39DAP/reference	1.21834	0.403
41DAP/reference	1.47678	0.014
42DAP/reference	1.10418	0.2
43DAP/reference	1.2481	0.163
47DAP/reference	1.09838	0.433
52DAP/reference	1.35593	0.029
57DAP/reference	1.0292	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.24662	0.305
27DAP/17DAP	1.45422	0.092
39DAP/27DAP	2.42795	0.046
41DAP/39DAP	0.29909	0.013
42DAP/41DAP	5.92663	0.002
43DAP/42DAP	4.44838	0.013
47DAP/43DAP	1.01746	1
52DAP/47DAP	1.32831	0.374
57DAP/52DAP	1.10662	0.899
57DAP/7DAP	15.98	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.70342	0.073
17DAP/reference	0.58515	0.011
27DAP/reference	0.80878	0.024
39DAP/reference	0.91778	0.198
41DAP/reference	0.72031	0.052
42DAP/reference	0.71334	0.06
43DAP/reference	0.74457	0.046
47DAP/reference	1.39881	0.06
52DAP/reference	0.75856	0.057
57DAP/reference	0.5629	0.014

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79036	0.124
17DAP/reference	0.83899	0.245
27DAP/reference	1.573	0.04
39DAP/reference	1.25017	0.194
41DAP/reference	1.08955	0.72
42DAP/reference	1.07373	0.826
43DAP/reference	1.22611	0.396
47DAP/reference	0.94722	0.349
52DAP/reference	1.12668	0.761
57DAP/reference	2.01275	0.06

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.57786	0.035
17DAP/reference	0.87331	0.358
27DAP/reference	0.58567	0.027
39DAP/reference	0.76625	0.037
41DAP/reference	0.80142	0.185
42DAP/reference	1.49742	0.007
43DAP/reference	1.83293	0.012
47DAP/reference	1.08683	0.966
52DAP/reference	1.39714	0.085
57DAP/reference	1.09824	0.539

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.85791	1
26DAP/20DAP	0.73905	0.512
34DAP/26DAP	1.30293	0.542
51DAP/34DAP	3.87508	0.021
52DAP/51DAP	0.63193	1
53DAP/52DAP	6.29179	0.077
55DAP/53DAP	1.04609	0.855
57DAP/55DAP	0.73654	0.154
62DAP/57DAP	0.56087	0.088
68DAP/62DAP	1.31789	0.767
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.25235	0.016

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.15167	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.2538
Mature Eggplant/Ripe Tomato	0.19759	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92237	0.944
1-1-2/M82	1.03305	1
12-2/M82	1.01757	1
12-4/M82	1.03852	1
1-3/M82	0.76469	0.501
2-1-1/M82	0.87566	0.683
2-1/M82	0.97191	1
2-6/M82	0.92342	0.501
3-2/M82	0.07991	0.384
4-1-1/M82	0.88178	1
4-1/M82	1.43896	1
4-3-2/M82	0.89164	1
4-3/M82	0.95964	1
5-3/M82	0.8891	0.642
6-2/M82	0.9841	1
6-3/M82	1.00687	1
7-1/M82	0.98267	1
7-2/M82	0.89332	0.796
9-3-2/M82	1.26609	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.71741	0.247
IL2-6/WTpooled	1.43004	0.788
IL7-5/WTpooled	0.54261	1
IL7-3/WTpooled	0.87564	1
IL12-4/WTpooled	0.97438	1
IL1-4/WTpooled	1.05431	1
WT/WTpooled	0.87753	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	0.80364	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09399	0.914
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	0.75475	0.079

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.04772
DC3000 delta B/DC3000 delta AB	1.71688

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

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

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

hybridization	ratio	FDR (corrected p value)
self-self	1.12174	1
Var 0h	1.35973	0.374
Var 12h I row2-row1	1.21013	0.506
Var 12h NI row2-row1	1.20891	0.649
Var 36h I row2-row1	1.11635	0.41
Var 36h NI row2-row1	0.99402	0.852
Var 60h I row2-row1	0.68899	0.293
Var 60h NI row2-row1	0.99254	1
Time course 0hI-0hNI	1.1536	0.262
Time course 12hI-12hNI	1.03895	0.816
Time course 36hI-36hNI	1.09689	0.19
Time course 60hI-60hNI	2.18822	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)	1.31638	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.19053	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.05696	0.381
Manapal/WT (red)	0.94486	0.181