Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.1.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84034	0.445
27DAP/17DAP	0.61278	0.051
39DAP/27DAP	1.02095	1
41DAP/39DAP	0.94575	0.739
42DAP/41DAP	1.43244	0.18
43DAP/42DAP	1.28804	0.816
47DAP/43DAP	0.75037	0.274
52DAP/47DAP	1.0552	0.865
57DAP/52DAP	0.96072	0.947

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90995	0.128
17DAP/reference	0.96145	0.24
27DAP/reference	0.9105	0.08
39DAP/reference	0.933	0.276
41DAP/reference	0.92463	0.154
42DAP/reference	0.8857	0.008
43DAP/reference	1.06059	0.252
47DAP/reference	0.86437	0.011
52DAP/reference	0.80647	0.015
57DAP/reference	0.80378	0.031

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02518	0.847
27DAP/17DAP	1.08348	0.912
39DAP/27DAP	0.68339	0.03
41DAP/39DAP	1.4557	0.748
42DAP/41DAP	0.89024	0.399
43DAP/42DAP	1.6579	0.027
47DAP/43DAP	0.96887	0.87
52DAP/47DAP	0.85827	0.397
57DAP/52DAP	1.38006	0.424
57DAP/7DAP	1.59462	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22934	0.119
17DAP/reference	1.1526	0.134
27DAP/reference	1.13113	0.197
39DAP/reference	1.20864	0.21
41DAP/reference	0.94876	0.394
42DAP/reference	0.92941	0.355
43DAP/reference	1.17623	0.105
47DAP/reference	0.91591	0.293
52DAP/reference	1.01843	0.74
57DAP/reference	0.84968	0.03

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91812	0.441
17DAP/reference	0.95221	0.447
27DAP/reference	0.85867	0.076
39DAP/reference	0.79382	0.02
41DAP/reference	0.85334	0.047
42DAP/reference	0.74426	0.016
43DAP/reference	0.93826	0.314
47DAP/reference	0.79216	0.01
52DAP/reference	0.84906	0.259
57DAP/reference	0.92465	0.384

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.45597	0.022
17DAP/reference	1.17156	0.298
27DAP/reference	1.08934	0.805
39DAP/reference	1.14657	0.059
41DAP/reference	1.0229	1
42DAP/reference	1.21297	0.189
43DAP/reference	1.22722	0.465
47DAP/reference	1.05782	0.339
52DAP/reference	1.46204	0.172
57DAP/reference	0.82546	0.021

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.20566	0.966
26DAP/20DAP	1.35746	0.415
34DAP/26DAP	1.3674	0.154
51DAP/34DAP	1.48676	0.043
52DAP/51DAP	1.16653	0.454
53DAP/52DAP	0.95902	0.891
55DAP/53DAP	0.76294	0.181
57DAP/55DAP	0.78064	0.427
62DAP/57DAP	1.66338	0.005
68DAP/62DAP	0.95549	0.863
68DAP/14DAP	1.50324	0.044

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.42166	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.61181	0.136
Mature Green Tomato/Ripe Tomato	0.67624	0.086
Immature Eggplant/Mature Eggplant	0.82205	0.134
Ripe Pepper/Ripe Tomato	4.53913	0.256
Mature Eggplant/Ripe Tomato	2.04721	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.20264	0.591
1-1-2/M82	1.09571
12-2/M82	0.97087	0.955
12-4/M82	1.11275	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.37298	0.405
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	1.97307
4-3/M82	1.52346
5-3/M82	1.05906	1
6-2/M82	N/A	N/A
6-3/M82	1.00745
7-1/M82	N/A	N/A
7-2/M82	1.10114	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.161	0.365
IL2-6/WTpooled	1.18427	0.395
IL7-5/WTpooled	1.11002
IL7-3/WTpooled	1.15027	1
IL12-4/WTpooled	0.78786	1
IL1-4/WTpooled	1	1
WT/WTpooled	0.80865	0.873

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	1.06551	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.88111	1
DC3000/delta hrp 6h	1.07832	1
DC3000/delta hrp 12h	1.00595	1
DC3000/delta hrp 24h	0.68835	0.042

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.37642
DC3000 delta B/DC3000 delta AB	0.40873	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.86903	1
Exp 36h	0.73139	0.504
Exp 60h	0.56284	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	1.10988	1
Var 0h	1.01391	1
Var 12h I row2-row1	0.82285	0.353
Var 12h NI row2-row1	1.03595	1
Var 36h I row2-row1	0.7279	0.805
Var 36h NI row2-row1	0.90366	0.584
Var 60h I row2-row1	1.16325	0.562
Var 60h NI row2-row1	0.98203	1
Time course 0hI-0hNI	0.90601	0.329
Time course 12hI-12hNI	0.97986	0.889
Time course 36hI-36hNI	0.87488	0.125
Time course 60hI-60hNI	0.12559	0.005

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)	1.02007	1
transgenic ySAMdc/azygous control (breaker)	0.68982	0.139
transgenic ySAMdc/azygous control (red)	1.18785	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02211	0.317

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.2859	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.32656	0.087
Manapal/WT (break)	1.64345	0.126
Manapal/WT (red)	1.07391	1