Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.20.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.36045	0.725
27DAP/17DAP	1.49566	0.714
39DAP/27DAP	1.10812	0.922
41DAP/39DAP	1.03955	0.949
42DAP/41DAP	1.25616	1
43DAP/42DAP	1.16331	1
47DAP/43DAP	0.79546	0.395
52DAP/47DAP	1.4369	0.396
57DAP/52DAP	1.28529	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05316	0.743
17DAP/reference	0.98014	0.701
27DAP/reference	0.99414	0.822
39DAP/reference	1.07013	0.857
41DAP/reference	0.85975	0.154
42DAP/reference	0.87716	0.02
43DAP/reference	0.92932	0.36
47DAP/reference	1.01185	1
52DAP/reference	0.85431	0.162
57DAP/reference	1.01798	0.845

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.54747	0.114
27DAP/17DAP	1.05162	0.919
39DAP/27DAP	1.08695	1
41DAP/39DAP	1.42095	0.497
42DAP/41DAP	0.88986	0.425
43DAP/42DAP	0.97886	0.774
47DAP/43DAP	1.07503	0.906
52DAP/47DAP	0.90924	0.739
57DAP/52DAP	1.17425	0.772
57DAP/7DAP	1.16893	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98102	0.613
17DAP/reference	1.13262	0.297
27DAP/reference	0.90305	0.066
39DAP/reference	0.99362	0.64
41DAP/reference	1.06648	0.812
42DAP/reference	1.10879	0.686
43DAP/reference	1.04099	0.707
47DAP/reference	0.87528	0.293
52DAP/reference	1.09992	0.139
57DAP/reference	1.00952	0.694

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81006	0.093
17DAP/reference	0.82519	0.047
27DAP/reference	0.92661	0.393
39DAP/reference	0.94759	0.416
41DAP/reference	0.70067	0.053
42DAP/reference	0.87363	0.261
43DAP/reference	0.78932	0.042
47DAP/reference	0.85715	0.09
52DAP/reference	0.90664	0.259
57DAP/reference	0.98136	0.68

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.171	0.23
17DAP/reference	0.90651	0.433
27DAP/reference	1.15163	0.179
39DAP/reference	1.09959	0.218
41DAP/reference	1.09042	0.637
42DAP/reference	0.84086	0.172
43DAP/reference	0.85283	0.206
47DAP/reference	0.93156	0.383
52DAP/reference	0.9778	0.637
57DAP/reference	0.88306	0.217

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.13943	0.966
26DAP/20DAP	1.30369	0.265
34DAP/26DAP	0.87877	0.627
51DAP/34DAP	1.33551	0.402
52DAP/51DAP	1.18206	0.15
53DAP/52DAP	0.7446	0.1
55DAP/53DAP	1.29236	0.781
57DAP/55DAP	0.94841	0.757
62DAP/57DAP	1.28523	0.185
68DAP/62DAP	1.15748	0.863
68DAP/14DAP	0.77136	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.04314	0.737

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.60798
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.31832	0.053
Ripe Pepper/Ripe Tomato	0.54729	0.293
Mature Eggplant/Ripe Tomato	0.7756	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.86071	0.907
1-1-2/M82	1.0709	1
12-2/M82	1.15019	0.327
12-4/M82	0.84963
1-3/M82	N/A	N/A
2-1-1/M82	0.90186	1
2-1/M82	0.88528	0.322
2-6/M82	0.81102	1
3-2/M82	1.3945
4-1-1/M82	1.02755	1
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.22004	1
5-3/M82	0.84226	0.49
6-2/M82	0.64212	0.481
6-3/M82	1.07369	1
7-1/M82	1.10343
7-2/M82	0.78356	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.70219	0.321
IL2-6/WTpooled	1.04113	0.788
IL7-5/WTpooled	1.33792
IL7-3/WTpooled	1.06055	1
IL12-4/WTpooled	0.94869	0.566
IL1-4/WTpooled	0.97868
WT/WTpooled	1.01459	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	1.50501	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00393	1
DC3000/delta hrp 6h	1.29304	0.95
DC3000/delta hrp 12h	1.00448	1
DC3000/delta hrp 24h	1.04168	0.567

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	3.60163

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.91537	1
Exp 36h	1.1938	1
Exp 60h	1.71856	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.12412	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.0645	0.613
Var 12h NI row2-row1	1.03978	1
Var 36h I row2-row1	1.11252	1
Var 36h NI row2-row1	1.31189	1
Var 60h I row2-row1	0.69076	0.285
Var 60h NI row2-row1	0.8778	0.318
Time course 0hI-0hNI	0.99838	1
Time course 12hI-12hNI	0.94616	0.695
Time course 36hI-36hNI	1.75893	0.005
Time course 60hI-60hNI	3.46175	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)	0.99821	1
transgenic ySAMdc/azygous control (breaker)	1.7267	0.162
transgenic ySAMdc/azygous control (red)	1.07093	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94463	0.044

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.02491	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.94428	1
Manapal/WT (break)	0.77335	0.299
Manapal/WT (red)	0.71106	0.183