Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.3.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84957	0.318
27DAP/17DAP	0.79998	0.257
39DAP/27DAP	0.79832	0.319
41DAP/39DAP	1.25434	0.498
42DAP/41DAP	1.0234	1
43DAP/42DAP	1.01848	0.937
47DAP/43DAP	1.24019	0.689
52DAP/47DAP	1.03456	0.851
57DAP/52DAP	1.06856	0.992

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90229	0.128
17DAP/reference	0.89795	0.091
27DAP/reference	0.89331	0.152
39DAP/reference	0.83091	0.078
41DAP/reference	0.80728	0.021
42DAP/reference	0.78596	0.012
43DAP/reference	0.92172	0.316
47DAP/reference	0.90369	0.014
52DAP/reference	0.86831	0.195
57DAP/reference	1.07554	0.724

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.33942	0.205
27DAP/17DAP	1.01917	0.988
39DAP/27DAP	0.86794	0.287
41DAP/39DAP	1.14219	0.735
42DAP/41DAP	0.84491	0.245
43DAP/42DAP	1.18502	0.446
47DAP/43DAP	1.00716	0.971
52DAP/47DAP	0.83824	0.159
57DAP/52DAP	1.02413	0.857
57DAP/7DAP	1.46814	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98772	0.682
17DAP/reference	1.04534	0.971
27DAP/reference	1.00677	1
39DAP/reference	1.17168	0.74
41DAP/reference	1.10578	0.491
42DAP/reference	1.32804	0.024
43DAP/reference	1.15168	0.432
47DAP/reference	1.0069	1
52DAP/reference	0.88762	0.106
57DAP/reference	1.04751	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98592	0.77
17DAP/reference	0.87233	0.099
27DAP/reference	0.92561	0.257
39DAP/reference	0.84142	0.117
41DAP/reference	0.84242	0.112
42DAP/reference	0.84718	0.035
43DAP/reference	1.02518	1
47DAP/reference	0.81089	0.015
52DAP/reference	0.89915	0.043
57DAP/reference	0.82922	0.018

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92774	0.29
17DAP/reference	0.95238	0.601
27DAP/reference	2.03106	0.12
39DAP/reference	1.25792	0.483
41DAP/reference	0.88451	0.025
42DAP/reference	0.83702	0.22
43DAP/reference	0.98654	0.712
47DAP/reference	0.87887	0.076
52DAP/reference	1.22756	0.779
57DAP/reference	1.06103	0.581

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09683	0.945
26DAP/20DAP	1.01712	1
34DAP/26DAP	1.02583	1
51DAP/34DAP	0.98125	0.863
52DAP/51DAP	0.86073	1
53DAP/52DAP	1.06972	0.901
55DAP/53DAP	1.27831	0.555
57DAP/55DAP	0.95658	0.799
62DAP/57DAP	0.92518	0.466
68DAP/62DAP	1.42631	0.481
68DAP/14DAP	1.35958	0.024

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.32263	0.131

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.00302	0.774
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.67845
Mature Eggplant/Ripe Tomato	0.52816

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.24004	1
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.12266
1-3/M82	0.62688
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.88788
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	0.95697
5-3/M82	1.05638	1
6-2/M82	0.4542
6-3/M82	0.65296
7-1/M82	N/A	N/A
7-2/M82	0.9084
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.72381	0.243
IL2-6/WTpooled	1.22296	0.659
IL7-5/WTpooled	0.84115
IL7-3/WTpooled	1.0003	1
IL12-4/WTpooled	1.21009	0.546
IL1-4/WTpooled	0.81618	0.834
WT/WTpooled	1.05941	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	0.73379	0.163

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93927	1
DC3000/delta hrp 6h	1.04071	1
DC3000/delta hrp 12h	0.82531	1
DC3000/delta hrp 24h	0.92315	0.464

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.05289	1
DC3000 delta B/DC3000 delta AB	0.61608

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.85825	1
Exp 36h	1.52257	1
Exp 60h	1.14496	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00651	1
Var 0h	0.90146	1
Var 12h I row2-row1	0.99949	1
Var 12h NI row2-row1	1.11062	1
Var 36h I row2-row1	0.73621	0.805
Var 36h NI row2-row1	1.23276	0.482
Var 60h I row2-row1	1.0487
Var 60h NI row2-row1	1.23357	0.904
Time course 0hI-0hNI	0.94609	0.721
Time course 12hI-12hNI	0.9001	0.177
Time course 36hI-36hNI	0.79175	0.024
Time course 60hI-60hNI	0.60034	0.015

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)	0.96968	0.485
transgenic ySAMdc/azygous control (breaker)	0.99123	1
transgenic ySAMdc/azygous control (red)	0.68213	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94422	0.186

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.83954	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.37297	0.084
Manapal/WT (break)	2.41651	0.14
Manapal/WT (red)	2.56475	0.15