Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.1.14.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85727	0.381
27DAP/17DAP	1.24254	1
39DAP/27DAP	1.14094	0.693
41DAP/39DAP	1.05717	0.978
42DAP/41DAP	1.07214	0.971
43DAP/42DAP	0.82048	0.599
47DAP/43DAP	1.02327	0.934
52DAP/47DAP	1.02031	0.916
57DAP/52DAP	1.43088	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94411	0.262
17DAP/reference	0.86332	0.057
27DAP/reference	0.95465	0.538
39DAP/reference	1.00747	1
41DAP/reference	0.76192	0.021
42DAP/reference	0.9019	0.052
43DAP/reference	0.91278	0.113
47DAP/reference	0.96684	0.322
52DAP/reference	1.18245	0.167
57DAP/reference	1.17858	0.021

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16541	0.558
27DAP/17DAP	1.05941	0.831
39DAP/27DAP	1.08046	0.663
41DAP/39DAP	1.0764	0.868
42DAP/41DAP	1.03267	1
43DAP/42DAP	0.79914	0.149
47DAP/43DAP	1.15483	0.735
52DAP/47DAP	1.01508	0.987
57DAP/52DAP	0.80387	0.555
57DAP/7DAP	1.5401	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84912	0.082
17DAP/reference	0.91175	0.192
27DAP/reference	1.10777	0.197
39DAP/reference	0.97023	0.474
41DAP/reference	1.00898	0.778
42DAP/reference	0.80437	0.063
43DAP/reference	0.98097	0.527
47DAP/reference	0.86988	0.222
52DAP/reference	0.92196	0.254
57DAP/reference	0.97627	0.458

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8364	0.204
17DAP/reference	0.8281	0.025
27DAP/reference	0.94435	0.317
39DAP/reference	1.05208	0.424
41DAP/reference	0.89865	0.169
42DAP/reference	0.92425	0.189
43DAP/reference	1.02949	0.969
47DAP/reference	0.92196	0.188
52DAP/reference	0.99826	0.713
57DAP/reference	0.87342	0.125

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93251	0.422
17DAP/reference	0.91055	0.262
27DAP/reference	1.10848	0.425
39DAP/reference	1.09066	0.254
41DAP/reference	0.87757	0.02
42DAP/reference	0.9692	0.671
43DAP/reference	0.9239	0.319
47DAP/reference	1.01978	1
52DAP/reference	0.84068	0.256
57DAP/reference	1.16151	0.47

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01669	1
26DAP/20DAP	0.9289	1
34DAP/26DAP	1.14859	1
51DAP/34DAP	1.10192	0.869
52DAP/51DAP	0.83221	0.151
53DAP/52DAP	1.11282	0.83
55DAP/53DAP	0.95817	0.735
57DAP/55DAP	1.19876	0.311
62DAP/57DAP	0.81071	0.28
68DAP/62DAP	1.03153	1
68DAP/14DAP	1.39004	0.487

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.67175	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.76636	0.226
Mature Green Tomato/Ripe Tomato	1.51386	0.399
Immature Eggplant/Mature Eggplant	0.98273	1
Ripe Pepper/Ripe Tomato	3.34221	0.233
Mature Eggplant/Ripe Tomato	1.94838	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.75881
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.8887	1
1-3/M82	0.83625
2-1-1/M82	1.01083
2-1/M82	N/A	N/A
2-6/M82	0.96583	1
3-2/M82	0.98446
4-1-1/M82	N/A	N/A
4-1/M82	1.00667
4-3-2/M82	N/A	N/A
4-3/M82	1.02725	1
5-3/M82	1.01264	1
6-2/M82	1.11533
6-3/M82	0.96261
7-1/M82	0.77799	0.803
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	1.32969	0.277
IL2-6/WTpooled	0.87303	0.358
IL7-5/WTpooled	1.18343	1
IL7-3/WTpooled	1.11291	1
IL12-4/WTpooled	0.93562	1
IL1-4/WTpooled	1.29972	1
WT/WTpooled	0.96519	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	0.95201	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94201	1
DC3000/delta hrp 6h	0.8595	0.95
DC3000/delta hrp 12h	0.97133	1
DC3000/delta hrp 24h	1.25331	0.077

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	2.00396	0.181

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.90765	0.623
Exp 60h	1.2412	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98733	1
Var 0h	1.07678	1
Var 12h I row2-row1	0.93432	0.418
Var 12h NI row2-row1	1.08175	0.649
Var 36h I row2-row1	1.02091	1
Var 36h NI row2-row1	0.65983	0.478
Var 60h I row2-row1	0.78676	0.582
Var 60h NI row2-row1	0.81899	0.818
Time course 0hI-0hNI	0.91579	0.489
Time course 12hI-12hNI	1.00766	0.867
Time course 36hI-36hNI	1.14742	0.006
Time course 60hI-60hNI	1.58388	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)	0.95223	0.362
transgenic ySAMdc/azygous control (breaker)	0.99508	1
transgenic ySAMdc/azygous control (red)	0.92916	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.18149	0.041

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.74367	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.12099	0.307
Manapal/WT (break)	1.03699	1
Manapal/WT (red)	0.81443	0.181