Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.17.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20759	0.534
27DAP/17DAP	2.95378	0.056
39DAP/27DAP	1.44089	0.24
41DAP/39DAP	1.05505	0.708
42DAP/41DAP	1.28613	0.73
43DAP/42DAP	1.39367	0.538
47DAP/43DAP	0.73972	0.274
52DAP/47DAP	1.06762	0.982
57DAP/52DAP	0.83644	0.86

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.34165	0.29
17DAP/reference	1.05786	0.546
27DAP/reference	1.14937	0.221
39DAP/reference	1.15774	0.593
41DAP/reference	1.17199	0.122
42DAP/reference	1.15251	0.072
43DAP/reference	1.10935	0.471
47DAP/reference	1.19425	0.11
52DAP/reference	1.27922	0.092
57DAP/reference	1.37437	0.012

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15989	0.119
27DAP/17DAP	1.23683	0.881
39DAP/27DAP	3.50585	0.034
41DAP/39DAP	0.37255	0.013
42DAP/41DAP	1.53291	0.008
43DAP/42DAP	1.5698	0.015
47DAP/43DAP	0.61001	0.01
52DAP/47DAP	1.23859	0.619
57DAP/52DAP	1.065	0.793
57DAP/7DAP	1.62429	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.70086	0.115
17DAP/reference	0.72388	0.016
27DAP/reference	0.74991	0.017
39DAP/reference	1.19392	0.062
41DAP/reference	0.67763	0.018
42DAP/reference	1.01609	0.828
43DAP/reference	1.45546	0.013
47DAP/reference	1.50679	0.016
52DAP/reference	1.18701	0.212
57DAP/reference	1.19701	0.268

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76794	0.06
17DAP/reference	0.92466	0.434
27DAP/reference	1.26657	0.109
39DAP/reference	1.33436	0.22
41DAP/reference	1.39112	0.01
42DAP/reference	1.3644	0.017
43DAP/reference	0.99885	0.748
47DAP/reference	1.38407	0.043
52DAP/reference	1.11567	0.444
57DAP/reference	0.83025	0.046

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7839	0.127
17DAP/reference	0.9276	0.499
27DAP/reference	0.86233	0.133
39DAP/reference	1.44167	0.885
41DAP/reference	0.86511	0.167
42DAP/reference	1.23527	0.4
43DAP/reference	1.35694	0.116
47DAP/reference	1.23031	0.133
52DAP/reference	1.00394	0.854
57DAP/reference	1.429	0.068

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.62178	0.966
26DAP/20DAP	1.19076	0.53
34DAP/26DAP	2.4021	0.106
51DAP/34DAP	2.36274	0.032
52DAP/51DAP	0.85332	0.151
53DAP/52DAP	1.02327	1
55DAP/53DAP	0.58322	0.029
57DAP/55DAP	0.83613	0.423
62DAP/57DAP	0.81988	0.681
68DAP/62DAP	1.24304	0.85
68DAP/14DAP	1.36839	0.636

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.77351	0.129

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.5196	0.106
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	3.19107
Mature Eggplant/Ripe Tomato	1.11097	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	2.02809	0.591
1-1-2/M82	1.00572	1
12-2/M82	1.18331	1
12-4/M82	0.97666	1
1-3/M82	2.28361	0.248
2-1-1/M82	1.3816	0.439
2-1/M82	1.81758	0.335
2-6/M82	1.05239	0.695
3-2/M82	5.39332	0.405
4-1-1/M82	0.70826	0.962
4-1/M82	0.72291
4-3-2/M82	0.7618	0.487
4-3/M82	0.76792	0.72
5-3/M82	1.03162	1
6-2/M82	2.3815	0.253
6-3/M82	0.99838	1
7-1/M82	N/A	N/A
7-2/M82	1.46571	0.385
9-3-2/M82	1.05737	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.69446
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.04206
IL12-4/WTpooled	1.68672	0.695
IL1-4/WTpooled	1.60806	1
WT/WTpooled	1.00871	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	1.0339	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.16799	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.96297
DC3000/delta hrp 24h	1.04079	0.743

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	N/A	N/A

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	1.03627
Var 0h	0.99907	1
Var 12h I row2-row1	0.6852	0.565
Var 12h NI row2-row1	1.26599	0.649
Var 36h I row2-row1	1.34921	0.339
Var 36h NI row2-row1	1.04632	1
Var 60h I row2-row1	1.13021	0.271
Var 60h NI row2-row1	0.78197	0.818
Time course 0hI-0hNI	0.97324	0.808
Time course 12hI-12hNI	0.84805	0.079
Time course 36hI-36hNI	0.90043	0.23
Time course 60hI-60hNI	1.12536	0.137

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)	0.71539	0.314
transgenic ySAMdc/azygous control (breaker)	1.62094	0.248
transgenic ySAMdc/azygous control (red)	1.07768	0.92

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	1.1295	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.87198	1
Manapal/WT (break)	0.66118	0.299
Manapal/WT (red)	0.76184	0.274