Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.13.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.47383	0.166
27DAP/17DAP	1.23339	0.742
39DAP/27DAP	1.10366	1
41DAP/39DAP	0.7946	0.215
42DAP/41DAP	0.87967	1
43DAP/42DAP	1.4092	0.147
47DAP/43DAP	0.72333	0.228
52DAP/47DAP	1.69868	0.198
57DAP/52DAP	1.22935	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93737	0.109
17DAP/reference	1.31652	0.018
27DAP/reference	1.31105	0.041
39DAP/reference	1.13522	0.377
41DAP/reference	1.16217	0.171
42DAP/reference	0.94098	0.259
43DAP/reference	1.07499	0.403
47DAP/reference	0.96048	0.279
52DAP/reference	0.92708	0.275
57DAP/reference	0.85064	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01315	0.871
27DAP/17DAP	1.17639	0.442
39DAP/27DAP	1.09041	0.483
41DAP/39DAP	1.07423	0.247
42DAP/41DAP	1.08813	0.635
43DAP/42DAP	1.1241	0.273
47DAP/43DAP	0.86107	0.16
52DAP/47DAP	1.23458	0.39
57DAP/52DAP	1.16796	0.606
57DAP/7DAP	1.51912	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9192	0.246
17DAP/reference	0.93933	0.072
27DAP/reference	0.89858	0.023
39DAP/reference	0.87221	0.23
41DAP/reference	0.99544	0.741
42DAP/reference	0.9875	0.582
43DAP/reference	0.96674	0.252
47DAP/reference	1.16981	0.493
52DAP/reference	1.05534	1
57DAP/reference	0.99586	0.694

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04616	0.741
17DAP/reference	1.15043	0.375
27DAP/reference	1.18901	0.212
39DAP/reference	0.93466	0.322
41DAP/reference	1.00547	0.683
42DAP/reference	0.93289	0.212
43DAP/reference	0.95915	0.438
47DAP/reference	1.03712	0.658
52DAP/reference	1.08283	0.343
57DAP/reference	1.14991	0.868

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05433	0.244
17DAP/reference	0.99436	0.792
27DAP/reference	1.08526	0.312
39DAP/reference	1.0442	0.422
41DAP/reference	0.95581	0.417
42DAP/reference	0.97466	0.287
43DAP/reference	0.8674	0.15
47DAP/reference	1.04502	0.877
52DAP/reference	0.92131	0.464
57DAP/reference	0.81027	0.064

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.73474	0.966
26DAP/20DAP	1.01744	1
34DAP/26DAP	0.82983	0.419
51DAP/34DAP	1.08828	0.936
52DAP/51DAP	0.92077	1
53DAP/52DAP	0.95372	0.75
55DAP/53DAP	0.9526	0.686
57DAP/55DAP	1.13876	0.865
62DAP/57DAP	0.95403	0.994
68DAP/62DAP	0.79076	0.227
68DAP/14DAP	0.91339	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.78976	0.072

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.42799
Mature Green Tomato/Ripe Tomato	1.43969	0.021
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.80746
Mature Eggplant/Ripe Tomato	0.1965

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.85371	1
12-2/M82	0.99263	0.955
12-4/M82	1.0776	1
1-3/M82	0.64203	0.33
2-1-1/M82	1.56204
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.84721
4-1-1/M82	1.38136
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	0.98542	1
6-2/M82	0.83655
6-3/M82	0.9619	1
7-1/M82	N/A	N/A
7-2/M82	1.12761	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.55128
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.98044	1
WT/WTpooled	1.16997

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	0.88047

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06452	0.921
DC3000/delta hrp 6h	1.24428	1
DC3000/delta hrp 12h	1.32213
DC3000/delta hrp 24h	0.77453	0.038

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	1.16027

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07471	1
Exp 36h	0.82434	0.623
Exp 60h	1.01712	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.93306	1
Var 0h	0.5469	0.936
Var 12h I row2-row1	0.94003	0.77
Var 12h NI row2-row1	1.07296	1
Var 36h I row2-row1	1.14863	0.283
Var 36h NI row2-row1	1.23273	0.482
Var 60h I row2-row1	1.09835	0.347
Var 60h NI row2-row1	1.02017	1
Time course 0hI-0hNI	1.21515	0.719
Time course 12hI-12hNI	0.81466	0.21
Time course 36hI-36hNI	0.81609	0.114
Time course 60hI-60hNI	0.142	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)	0.90601	0.362
transgenic ySAMdc/azygous control (breaker)	0.54295	0.137
transgenic ySAMdc/azygous control (red)	1.1432	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94397	0.227

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95575	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.80492	0.096
Manapal/WT (break)	0.69262	1
Manapal/WT (red)	1.23306	0.413