Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.12.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1632	0.463
27DAP/17DAP	0.47753	0.027
39DAP/27DAP	0.9142	0.573
41DAP/39DAP	0.48845	0.041
42DAP/41DAP	0.94467	1
43DAP/42DAP	1.03506	0.937
47DAP/43DAP	0.59886	0.086
52DAP/47DAP	1.14857	0.773
57DAP/52DAP	0.93683	0.908

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.71892	0.07
17DAP/reference	0.45341	0.009
27DAP/reference	0.44446	0.012
39DAP/reference	0.41375	0.012
41DAP/reference	0.2526	0.008
42DAP/reference	0.31629	0.001
43DAP/reference	0.20872	0.012
47DAP/reference	0.17606	0.001
52DAP/reference	0.20032	0.012
57DAP/reference	0.26966	0.007

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.39158	0.044
27DAP/17DAP	0.81143	0.121
39DAP/27DAP	0.66392	0.037
41DAP/39DAP	1.12452	0.748
42DAP/41DAP	0.94736	0.52
43DAP/42DAP	0.95695	0.618
47DAP/43DAP	0.95081	0.597
52DAP/47DAP	1.01029	1
57DAP/52DAP	0.89771	0.289
57DAP/7DAP	0.8069	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06588	0.747
17DAP/reference	0.82376	0.039
27DAP/reference	0.49261	0.01
39DAP/reference	0.43701	0.011
41DAP/reference	0.32335	0.009
42DAP/reference	0.30222	0.01
43DAP/reference	0.3115	0.01
47DAP/reference	0.22183	0.026
52DAP/reference	0.36265	0.011
57DAP/reference	0.36073	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.4514	0.008
17DAP/reference	0.46052	0.009
27DAP/reference	0.6287	0.062
39DAP/reference	0.34864	0.009
41DAP/reference	0.39054	0.006
42DAP/reference	0.32819	0.01
43DAP/reference	0.17156	0.002
47DAP/reference	0.22997	0.007
52DAP/reference	0.19367	0.003
57DAP/reference	0.13373	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.13315	0.019
17DAP/reference	1.82878	0.111
27DAP/reference	1.31736	0.052
39DAP/reference	1.07305	0.752
41DAP/reference	0.70145	0.024
42DAP/reference	0.50804	0.016
43DAP/reference	0.53336	0.019
47DAP/reference	0.33487	0.004
52DAP/reference	0.46094	0.068
57DAP/reference	1.36869	0.339

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9218	1
26DAP/20DAP	1.10949	0.7
34DAP/26DAP	0.86359	0.228
51DAP/34DAP	0.54075	0.049
52DAP/51DAP	1.04227	0.596
53DAP/52DAP	0.89184	0.242
55DAP/53DAP	0.97572	0.746
57DAP/55DAP	0.91493	0.612
62DAP/57DAP	1.22833	0.185
68DAP/62DAP	0.81169	0.579
68DAP/14DAP	0.44378	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.65689	0.027

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.72979	0.058
Mature Green Tomato/Ripe Tomato	10.945	0.015
Immature Eggplant/Mature Eggplant	0.51116	0.058
Ripe Pepper/Ripe Tomato	24.6999	0.258
Mature Eggplant/Ripe Tomato	31.531	0.26

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	0.69133
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	0.79802
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	1.17934
4-1-1/M82	N/A	N/A
4-1/M82	0.8257
4-3-2/M82	0.93994
4-3/M82	N/A	N/A
5-3/M82	2.24545
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.80662
7-2/M82	1.01915
9-3-2/M82	1.18458	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.80811	0.247
IL2-6/WTpooled	1.00939	1
IL7-5/WTpooled	3.08239	0.792
IL7-3/WTpooled	0.84585	0.294
IL12-4/WTpooled	0.96781	1
IL1-4/WTpooled	1.00451	1
WT/WTpooled	0.97481	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	1.03304	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00111
DC3000/delta hrp 6h	0.89619	0.95
DC3000/delta hrp 12h	1.132	1
DC3000/delta hrp 24h	1.03574	0.604

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.86358	0.66
DC3000 delta B/DC3000 delta AB	0.52456	0.023

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00274	1
Exp 36h	0.96868	0.943
Exp 60h	0.94806	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99929	1
Var 0h	0.85497	1
Var 12h I row2-row1	0.98812	1
Var 12h NI row2-row1	0.99505	1
Var 36h I row2-row1	0.9846	1
Var 36h NI row2-row1	1.61111	1
Var 60h I row2-row1	1.25608	0.562
Var 60h NI row2-row1	0.97709	0.977
Time course 0hI-0hNI	1.00028	1
Time course 12hI-12hNI	1.03144	0.72
Time course 36hI-36hNI	1.05194	0.063
Time course 60hI-60hNI	0.85859	0.319

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)	1.15736	0.699
transgenic ySAMdc/azygous control (breaker)	4.22019	0.162
transgenic ySAMdc/azygous control (red)	1.50502	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.42503	0.071

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01185	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	26.2039	0.087
Manapal/WT (break)	15.714	0.123
Manapal/WT (red)	3.69659	0.413