Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.17.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.37706	0.403
27DAP/17DAP	1.97213	0.688
39DAP/27DAP	1.09231	0.853
41DAP/39DAP	1.13156	0.372
42DAP/41DAP	1.12816	0.825
43DAP/42DAP	0.92597	0.829
47DAP/43DAP	0.98338	0.89
52DAP/47DAP	0.82693	0.545
57DAP/52DAP	1.04328	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9011	0.336
17DAP/reference	0.83611	0.111
27DAP/reference	1.07967	0.709
39DAP/reference	0.98934	0.841
41DAP/reference	0.91506	0.341
42DAP/reference	0.9883	0.413
43DAP/reference	0.97396	0.675
47DAP/reference	0.95101	0.322
52DAP/reference	1.67565	0.092
57DAP/reference	1.1582	0.259

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.77346	0.164
27DAP/17DAP	1.10649	0.546
39DAP/27DAP	1.73222	0.227
41DAP/39DAP	2.54374	0.008
42DAP/41DAP	0.69868	0.007
43DAP/42DAP	0.60178	0.022
47DAP/43DAP	1.12688	0.471
52DAP/47DAP	1.02547	0.962
57DAP/52DAP	0.71554	0.205
57DAP/7DAP	1.08568	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79701	0.088
17DAP/reference	0.89125	0.167
27DAP/reference	0.98595	0.571
39DAP/reference	0.82538	0.073
41DAP/reference	0.92974	0.326
42DAP/reference	0.83303	0.077
43DAP/reference	0.95403	0.385
47DAP/reference	0.93941	0.383
52DAP/reference	0.77014	0.023
57DAP/reference	0.84427	0.074

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.34857	0.559
17DAP/reference	0.85533	0.164
27DAP/reference	1.04877	0.79
39DAP/reference	1.0106	0.702
41DAP/reference	1.09637	0.491
42DAP/reference	1.16227	0.398
43DAP/reference	1.03384	0.846
47DAP/reference	0.96113	0.41
52DAP/reference	0.98817	0.576
57DAP/reference	0.95651	0.488

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92587	0.311
17DAP/reference	0.85508	0.286
27DAP/reference	0.98667	0.691
39DAP/reference	0.80356	0.063
41DAP/reference	0.94973	0.459
42DAP/reference	1.01922	0.923
43DAP/reference	0.874	0.294
47DAP/reference	1.04504	1
52DAP/reference	1.23345	0.657
57DAP/reference	1.19207	0.362

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.95225	0.015
26DAP/20DAP	0.83587	0.317
34DAP/26DAP	1.05633	1
51DAP/34DAP	0.77593	0.292
52DAP/51DAP	0.92736	1
53DAP/52DAP	0.88585	0.553
55DAP/53DAP	1.27437	0.653
57DAP/55DAP	0.88354	0.468
62DAP/57DAP	1.0574	1
68DAP/62DAP	1.4411	0.945
68DAP/14DAP	1.10724	0.656

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.27454	0.229

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.47596	0.023
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.82767
Mature Eggplant/Ripe Tomato	0.48948	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.39152
12-2/M82	N/A	N/A
12-4/M82	0.88914	0.619
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	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.83491
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.90091
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	0.93202	1
IL2-6/WTpooled	0.77022	1
IL7-5/WTpooled	0.97641	1
IL7-3/WTpooled	0.80613	0.418
IL12-4/WTpooled	0.95976	1
IL1-4/WTpooled	1.04991	1
WT/WTpooled	0.91982	0.962

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	2.34845	0.083

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00562	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.00392	1
DC3000/delta hrp 24h	0.77888	0.073

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.79589	0.047
DC3000 delta B/DC3000 delta AB	3.59069	0.02

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	1.01536	1
Var 0h	2.24054	0.936
Var 12h I row2-row1	0.84925	0.705
Var 12h NI row2-row1	2.52411	0.266
Var 36h I row2-row1	1.43442	0.742
Var 36h NI row2-row1	0.44373	0.478
Var 60h I row2-row1	0.78918	0.582
Var 60h NI row2-row1	0.56755	0.329
Time course 0hI-0hNI	1.78116	0.574
Time course 12hI-12hNI	1.73246	0.56
Time course 36hI-36hNI	7.76359	0.004
Time course 60hI-60hNI	40.3727	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)	0.77281	1

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	1.35211	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.9117	1
Manapal/WT (break)	1.39973	1
Manapal/WT (red)	1.63943	0.164