Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.13.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.28144	0.014
27DAP/17DAP	0.81116	0.641
39DAP/27DAP	1.08952	1
41DAP/39DAP	0.97199	0.781
42DAP/41DAP	1.03752	1
43DAP/42DAP	1.08078	0.945
47DAP/43DAP	1.03878	0.953
52DAP/47DAP	0.84601	0.598
57DAP/52DAP	0.69062	0.759

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97343	0.661
17DAP/reference	1.00001	1
27DAP/reference	0.91122	0.068
39DAP/reference	0.96579	0.651
41DAP/reference	1.08145	0.111
42DAP/reference	0.87049	0.001
43DAP/reference	0.94691	0.222
47DAP/reference	0.8487	0.005
52DAP/reference	0.84496	0.036
57DAP/reference	0.88968	0.091

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91258	0.35
27DAP/17DAP	1.05908	0.822
39DAP/27DAP	1.09813	0.596
41DAP/39DAP	0.90769	0.696
42DAP/41DAP	1.00303	0.902
43DAP/42DAP	1.09278	0.112
47DAP/43DAP	1.00754	0.973
52DAP/47DAP	0.98459	0.925
57DAP/52DAP	1.00385	1
57DAP/7DAP	1.03592	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90526	0.27
17DAP/reference	1.44262	0.006
27DAP/reference	1.32294	0.01
39DAP/reference	1.20706	0.042
41DAP/reference	1.28377	0.177
42DAP/reference	1.31025	0.021
43DAP/reference	1.32797	0.083
47DAP/reference	0.85372	0.293
52DAP/reference	0.94349	0.435
57DAP/reference	0.81701	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75758	0.011
17DAP/reference	0.69627	0.004
27DAP/reference	0.84689	0.139
39DAP/reference	0.68815	0.013
41DAP/reference	0.82688	0.148
42DAP/reference	0.88315	0.108
43DAP/reference	0.73369	0.036
47DAP/reference	0.93738	0.053
52DAP/reference	0.76167	0.004
57DAP/reference	0.80392	0.008

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96267	0.183
17DAP/reference	0.95923	0.592
27DAP/reference	1.53432	0.039
39DAP/reference	1.28922	0.342
41DAP/reference	1.12537	0.369
42DAP/reference	0.99029	0.816
43DAP/reference	0.92634	0.348
47DAP/reference	0.64152	0.005
52DAP/reference	1.43256	0.363
57DAP/reference	0.71032	0.058

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00259	1
26DAP/20DAP	0.82229	0.512
34DAP/26DAP	0.98789	1
51DAP/34DAP	1.07458	0.692
52DAP/51DAP	1.05492	0.758
53DAP/52DAP	0.99522	0.96
55DAP/53DAP	0.91056	0.592
57DAP/55DAP	1.1431	0.543
62DAP/57DAP	0.87515	0.162
68DAP/62DAP	0.79287	0.378
68DAP/14DAP	0.69103	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.91781	0.239

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.13758
Mature Eggplant/Ripe Tomato	1.26022	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	0.95737
2-1/M82	N/A	N/A
2-6/M82	1.00941
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.16382
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.83386	0.447
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
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	0.3701
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.33709	0.362
IL12-4/WTpooled	0.80036	0.71
IL1-4/WTpooled	0.95084
WT/WTpooled	0.92175	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	0.59362	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00111	1
DC3000/delta hrp 6h	1.16567	1
DC3000/delta hrp 12h	0.65705	1
DC3000/delta hrp 24h	19.0496	0.025

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.90648	0.047
DC3000 delta B/DC3000 delta AB	1.09139	0.433

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.85403	0.749
Exp 60h	1.62848	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95729	1
Var 0h	0.62568	0.933
Var 12h I row2-row1	1.45192	0.187
Var 12h NI row2-row1	0.6267	0.546
Var 36h I row2-row1	1.036	1
Var 36h NI row2-row1	1.70423	0.237
Var 60h I row2-row1	1.06362	0.276
Var 60h NI row2-row1	1.66581	0.793
Time course 0hI-0hNI	0.81307	0.211
Time course 12hI-12hNI	0.7332	0.173
Time course 36hI-36hNI	0.85443	0.156
Time course 60hI-60hNI	0.24523	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)	1.37283	0.482
transgenic ySAMdc/azygous control (breaker)	1.35726	0.165
transgenic ySAMdc/azygous control (red)	0.86889	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95699	0.168

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.58454	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	0.67315	0.299
Manapal/WT (red)	0.65388	0.274