Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.2.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	10.8383	0.033
27DAP/17DAP	2.27382	0.261
39DAP/27DAP	1.38442	0.542
41DAP/39DAP	0.64596	0.171
42DAP/41DAP	1.16695	0.882
43DAP/42DAP	1.39	1
47DAP/43DAP	0.63405	0.117
52DAP/47DAP	0.56616	0.133
57DAP/52DAP	2.06823	0.839

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.56267	0.029
17DAP/reference	0.79867	0.012
27DAP/reference	1.2097	0.152
39DAP/reference	1.39741	0.034
41DAP/reference	1.13428	0.312
42DAP/reference	1.33994	0.001
43DAP/reference	1.03917	0.547
47DAP/reference	1.23722	0.003
52DAP/reference	1.13869	0.388
57DAP/reference	1.21634	0.012

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	3.05567	0.036
27DAP/17DAP	1.63735	0.295
39DAP/27DAP	0.98519	0.87
41DAP/39DAP	1.4817	0.887
42DAP/41DAP	1.06762	0.841
43DAP/42DAP	1.10655	0.83
47DAP/43DAP	0.88512	0.734
52DAP/47DAP	1.53566	0.374
57DAP/52DAP	0.79964	0.244
57DAP/7DAP	4.35241	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97493	0.55
17DAP/reference	1.36186	0.025
27DAP/reference	1.78789	0.014
39DAP/reference	N/A	N/A
41DAP/reference	1.7563
42DAP/reference	N/A	N/A
43DAP/reference	2.16422
47DAP/reference	1.43301	0.063
52DAP/reference	1.41641	0.021
57DAP/reference	1.26129	0.061

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.4595	0.007
17DAP/reference	1.08606	0.257
27DAP/reference	2.04549	0.017
39DAP/reference	2.17459	0.012
41DAP/reference	1.79955	0.005
42DAP/reference	2.12282	0.007
43DAP/reference	1.02465	0.494
47DAP/reference	1.34776	0.065
52DAP/reference	2.19759	0.006
57DAP/reference	0.94295	0.433

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.39202	0.087
17DAP/reference	0.86534	0.364
27DAP/reference	1.46183	0.096
39DAP/reference	1.78313	0.008
41DAP/reference	1.01437	0.939
42DAP/reference	1.52444	0.008
43DAP/reference	1.57265	0.123
47DAP/reference	1.23664	0.028
52DAP/reference	1.35692	0.233
57DAP/reference	1.54475	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05242	1
26DAP/20DAP	1.19084	0.574
34DAP/26DAP	0.78281	0.095
51DAP/34DAP	0.51896	0.058
52DAP/51DAP	0.88755	0.151
53DAP/52DAP	1.95733	0.03
55DAP/53DAP	0.71136	0.023
57DAP/55DAP	0.88928	0.539
62DAP/57DAP	0.917	0.162
68DAP/62DAP	2.45621	0.017
68DAP/14DAP	2.51867	0.028

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	8.65532	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	2.34011	0.044
Immature Eggplant/Mature Eggplant	0.45232	0.067
Ripe Pepper/Ripe Tomato	0.08176	0.224
Mature Eggplant/Ripe Tomato	1.18077	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.07282	0.877
1-1-2/M82	1.60349	1
12-2/M82	1.267	1
12-4/M82	1.83535	1
1-3/M82	1.12418	1
2-1-1/M82	1.31213	0.457
2-1/M82	0.81424	0.74
2-6/M82	0.92983	1
3-2/M82	1.84669	0.463
4-1-1/M82	1.39886	1
4-1/M82	3.35612	0.853
4-3-2/M82	1.21338	1
4-3/M82	2.11119	0.268
5-3/M82	0.70134	1
6-2/M82	3.50156	0.235
6-3/M82	1.10578	1
7-1/M82	0.17336	0.408
7-2/M82	0.37297	0.565
9-3-2/M82	1.16853	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.90994	1
IL2-6/WTpooled	1.20801
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.00976
IL12-4/WTpooled	0.84725	1
IL1-4/WTpooled	0.95274	1
WT/WTpooled	1.33306	0.686

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	0.82545	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00931	1
DC3000/delta hrp 6h	0.33507
DC3000/delta hrp 12h	0.98486	1
DC3000/delta hrp 24h	1.05986	0.535

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.91045	0.232
DC3000 delta B/DC3000 delta AB	0.91988	0.178

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.86404	1
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	1.03109	1
Var 0h	0.95506	1
Var 12h I row2-row1	0.88557	0.418
Var 12h NI row2-row1	1.12569	0.649
Var 36h I row2-row1	1.04558	0.489
Var 36h NI row2-row1	1.07335	0.482
Var 60h I row2-row1	1.09063	1
Var 60h NI row2-row1	1.08909	1
Time course 0hI-0hNI	1.4244	0.852
Time course 12hI-12hNI	0.96427	0.802
Time course 36hI-36hNI	0.85073	0.052
Time course 60hI-60hNI	0.77569	0.081

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)	1.06159	0.798
transgenic ySAMdc/azygous control (breaker)	0.97622	1
transgenic ySAMdc/azygous control (red)	0.91418	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07642	0.13

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.18437	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.01844	1
Manapal/WT (break)	0.9048	1
Manapal/WT (red)	1.6763	0.222