Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-3.3.12.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00728	0.938
27DAP/17DAP	0.54116	0.027
39DAP/27DAP	0.74769	0.335
41DAP/39DAP	0.74738	0.145
42DAP/41DAP	0.85935	1
43DAP/42DAP	1.09136	1
47DAP/43DAP	0.75786	0.295
52DAP/47DAP	1.10777	0.879
57DAP/52DAP	0.90675	0.919

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23253	0.252
17DAP/reference	0.68063	0.01
27DAP/reference	0.85204	0.147
39DAP/reference	0.63764	0.026
41DAP/reference	0.50161	0.008
42DAP/reference	0.57872	0.001
43DAP/reference	0.28144	0.012
47DAP/reference	0.21541	0.001
52DAP/reference	0.27811	0.012
57DAP/reference	0.35528	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.42934	0.074
27DAP/17DAP	1.00563	0.969
39DAP/27DAP	0.45669	0.028
41DAP/39DAP	1.00392	0.914
42DAP/41DAP	0.86125	0.201
43DAP/42DAP	0.56467	0.024
47DAP/43DAP	0.97861	0.911
52DAP/47DAP	0.99297	0.919
57DAP/52DAP	0.85422	0.334
57DAP/7DAP	0.2697	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00671	1
17DAP/reference	0.97411	0.389
27DAP/reference	0.94366	0.171
39DAP/reference	0.71877	0.011
41DAP/reference	0.6552	0.035
42DAP/reference	0.79552	0.014
43DAP/reference	0.66348	0.011
47DAP/reference	0.3906	0.044
52DAP/reference	0.64971	0.012
57DAP/reference	0.62487	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94346	0.548
17DAP/reference	1.19321	0.216
27DAP/reference	0.75878	0.033
39DAP/reference	0.57269	0.009
41DAP/reference	0.64243	0.032
42DAP/reference	0.6025	0.013
43DAP/reference	0.57325	0.014
47DAP/reference	0.37589	0.007
52DAP/reference	0.42472	0.003
57DAP/reference	0.34547	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.46051	0.015
17DAP/reference	1.74523	0.092
27DAP/reference	1.3717	0.019
39DAP/reference	0.99012	0.693
41DAP/reference	0.94411	0.293
42DAP/reference	0.80544	0.028
43DAP/reference	0.72238	0.038
47DAP/reference	0.39887	0.004
52DAP/reference	0.75561	0.107
57DAP/reference	1.21466	0.604

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.65069	1
26DAP/20DAP	1.02318	1
34DAP/26DAP	0.97285	0.945
51DAP/34DAP	0.57606	0.049
52DAP/51DAP	1.03671	0.836
53DAP/52DAP	0.73169	0.049
55DAP/53DAP	0.76362	0.037
57DAP/55DAP	1.02056	1
62DAP/57DAP	1.41072	0.158
68DAP/62DAP	0.57657	0.039
68DAP/14DAP	0.39032	0.09

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.35318	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.92302	0.058
Mature Green Tomato/Ripe Tomato	6.15849	0.015
Immature Eggplant/Mature Eggplant	0.29726	0.062
Ripe Pepper/Ripe Tomato	17.4428	N/A
Mature Eggplant/Ripe Tomato	23.4267	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04925	1
1-1-2/M82	0.78263	0.958
12-2/M82	1.34675	N/A
12-4/M82	0.67092	N/A
1-3/M82	0.75493	0.33
2-1-1/M82	0.88672	0.92
2-1/M82	N/A	N/A
2-6/M82	1.00027	1
3-2/M82	N/A	N/A
4-1-1/M82	0.57888	N/A
4-1/M82	1.22667	1
4-3-2/M82	1.06945	1
4-3/M82	N/A	N/A
5-3/M82	1.01209	0.572
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.95655	0.881
9-3-2/M82	0.86001	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.96368	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.07396	1
IL12-4/WTpooled	1.05368	0.695
IL1-4/WTpooled	0.74555	N/A
WT/WTpooled	0.93275	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	1.00812	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.968	1
DC3000/delta hrp 6h	1.31922	1
DC3000/delta hrp 12h	1.5965	1
DC3000/delta hrp 24h	0.90607	0.438

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.54588	0.026
DC3000 delta B/DC3000 delta AB	0.41035	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98473	1
Exp 36h	0.69642	0.504
Exp 60h	0.69731	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00682	1
Var 0h	0.77434	1
Var 12h I row2-row1	1.27496	0.654
Var 12h NI row2-row1	0.93112	0.494
Var 36h I row2-row1	0.80599	0.805
Var 36h NI row2-row1	1.01478	1
Var 60h I row2-row1	1.49987	0.562
Var 60h NI row2-row1	0.91582	0.866
Time course 0hI-0hNI	1.05386	0.662
Time course 12hI-12hNI	1.00864	0.867
Time course 36hI-36hNI	0.97662	0.514
Time course 60hI-60hNI	0.16279	0.006

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)	0.7564	0.3
transgenic ySAMdc/azygous control (breaker)	1.80802	0.248
transgenic ySAMdc/azygous control (red)	0.98182	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.55926	0.058

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.71535	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	5.14032	0.083
Manapal/WT (break)	5.74504	0.123
Manapal/WT (red)	5.62015	0.164