Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.16.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09289	0.545
27DAP/17DAP	1.12208	0.836
39DAP/27DAP	0.87061	0.458
41DAP/39DAP	1.18707	0.522
42DAP/41DAP	1.23802	0.466
43DAP/42DAP	1.08445	1
47DAP/43DAP	1.04834	0.873
52DAP/47DAP	0.94707	0.837
57DAP/52DAP	0.9984	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94657	0.277
17DAP/reference	1.01827	0.606
27DAP/reference	1.02693	0.539
39DAP/reference	1.06646	0.035
41DAP/reference	1.02769	0.667
42DAP/reference	0.97352	0.163
43DAP/reference	0.99386	0.861
47DAP/reference	0.98511	0.445
52DAP/reference	0.94299	0.283
57DAP/reference	0.90486	0.124

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91994	0.415
27DAP/17DAP	1.09007	0.78
39DAP/27DAP	1.53065	0.046
41DAP/39DAP	0.64353	0.022
42DAP/41DAP	1.19022	0.007
43DAP/42DAP	1.53179	0.015
47DAP/43DAP	0.96513	0.606
52DAP/47DAP	1.21457	0.367
57DAP/52DAP	0.92145	0.454
57DAP/7DAP	1.05373	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84848	0.104
17DAP/reference	0.8494	0.011
27DAP/reference	0.80767	0.01
39DAP/reference	0.88801	0.011
41DAP/reference	0.89362	0.06
42DAP/reference	0.85695	0.034
43DAP/reference	0.84538	0.012
47DAP/reference	0.7862	0.033
52DAP/reference	0.83524	0.012
57DAP/reference	0.87928	0.038

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94844	0.457
17DAP/reference	0.98656	0.536
27DAP/reference	0.9153	0.111
39DAP/reference	0.96937	0.428
41DAP/reference	0.92381	0.205
42DAP/reference	0.87556	0.015
43DAP/reference	1.03302	0.865
47DAP/reference	0.94757	0.141
52DAP/reference	0.96363	0.143
57DAP/reference	1.07196	0.314

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81889	0.049
17DAP/reference	0.93426	0.364
27DAP/reference	0.85346	0.046
39DAP/reference	0.81771	0.016
41DAP/reference	0.856	0.046
42DAP/reference	0.78899	0.025
43DAP/reference	0.79914	0.037
47DAP/reference	1.02048	0.966
52DAP/reference	0.78459	0.103
57DAP/reference	0.67341	0.018

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99336	1
26DAP/20DAP	0.92612	0.512
34DAP/26DAP	1.1726	1
51DAP/34DAP	0.86892	0.143
52DAP/51DAP	1.22912	0.232
53DAP/52DAP	1.00654	1
55DAP/53DAP	1.15754	0.229
57DAP/55DAP	1.14267	0.87
62DAP/57DAP	0.95769	0.994
68DAP/62DAP	1.03605	0.971
68DAP/14DAP	0.86074	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.83037	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.63734	0.058
Mature Green Tomato/Ripe Tomato	0.70569	0.045
Immature Eggplant/Mature Eggplant	1.0006	1
Ripe Pepper/Ripe Tomato	0.6466
Mature Eggplant/Ripe Tomato	0.80668	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97608	0.944
1-1-2/M82	0.87494
12-2/M82	0.94077	0.678
12-4/M82	1.05215	1
1-3/M82	0.76673	0.339
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.13218	0.695
3-2/M82	0.8629
4-1-1/M82	0.93566	1
4-1/M82	0.79735	1
4-3-2/M82	0.87571	0.698
4-3/M82	0.72314	0.396
5-3/M82	0.97243	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.93883	0.803
7-2/M82	0.92836	0.381
9-3-2/M82	0.84308

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.16617	0.456
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.96981	1
IL12-4/WTpooled	1.15409	0.538
IL1-4/WTpooled	0.86633
WT/WTpooled	1.02457	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	1.02431	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94557	0.868
DC3000/delta hrp 6h	1.14466	1
DC3000/delta hrp 12h	1.06764	1
DC3000/delta hrp 24h	1.02914	0.69

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.06232	0.515
DC3000 delta B/DC3000 delta AB	1.14761	0.256

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.9595	0.82
Exp 60h	1.03857	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99832	1
Var 0h	0.8316	0.933
Var 12h I row2-row1	1.06058	0.379
Var 12h NI row2-row1	0.88004	0.627
Var 36h I row2-row1	0.93707	1
Var 36h NI row2-row1	1.15931	1
Var 60h I row2-row1	1.23257	1
Var 60h NI row2-row1	1.13325	0.904
Time course 0hI-0hNI	1.08591	0.486
Time course 12hI-12hNI	0.94183	0.357
Time course 36hI-36hNI	0.93016	0.162
Time course 60hI-60hNI	1.91813	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)	0.84341	0.33
transgenic ySAMdc/azygous control (breaker)	1.38238	0.165
transgenic ySAMdc/azygous control (red)	1.14214	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97165	0.305

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.94127	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.76638	0.172
Manapal/WT (break)	0.68825	0.299
Manapal/WT (red)	0.97504	0.424