Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-4.1.12.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04545	0.911
27DAP/17DAP	1.05882	1
39DAP/27DAP	1.04982	1
41DAP/39DAP	1.09781	0.929
42DAP/41DAP	1.16402	0.888
43DAP/42DAP	0.98225	0.93
47DAP/43DAP	0.91847	0.701
52DAP/47DAP	1.27373	0.541
57DAP/52DAP	0.93111	0.919

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05317	0.685
17DAP/reference	1.12265	0.057
27DAP/reference	1.03896	0.672
39DAP/reference	1.0229	0.691
41DAP/reference	1.26922	0.012
42DAP/reference	0.9611	0.25
43DAP/reference	1.11623	0.163
47DAP/reference	1.0836	0.295
52DAP/reference	0.89963	0.049
57DAP/reference	0.86278	0.022

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9283	0.428
27DAP/17DAP	1.1153	0.621
39DAP/27DAP	0.9369	0.594
41DAP/39DAP	1.05836	0.763
42DAP/41DAP	0.87258	0.181
43DAP/42DAP	0.95039	0.558
47DAP/43DAP	1.01664	0.95
52DAP/47DAP	1.07385	0.823
57DAP/52DAP	1.08235	0.666
57DAP/7DAP	0.78542	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90828	0.27
17DAP/reference	0.95	0.124
27DAP/reference	0.90576	0.125
39DAP/reference	0.93692	0.23
41DAP/reference	0.95373	0.326
42DAP/reference	0.85873	0.014
43DAP/reference	0.89251	0.046
47DAP/reference	0.94389	0.383
52DAP/reference	0.9551	0.332
57DAP/reference	1.05602	0.907

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19182	0.265
17DAP/reference	1.23481	0.06
27DAP/reference	1.04984	0.888
39DAP/reference	1.12893	0.543
41DAP/reference	1.05857	0.925
42DAP/reference	1.08169	0.879
43DAP/reference	1.15902	0.362
47DAP/reference	1.03494	0.89
52DAP/reference	1.15459	0.092
57DAP/reference	1.38976	0.01

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91024	0.065
17DAP/reference	1.0162	1
27DAP/reference	1.06343	0.531
39DAP/reference	1.00027	0.819
41DAP/reference	1.01452	1
42DAP/reference	1.01998	1
43DAP/reference	1.01063	0.767
47DAP/reference	0.95771	0.434
52DAP/reference	1.04619	0.735
57DAP/reference	0.86846	0.174

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.8534	1
26DAP/20DAP	1.02055	1
34DAP/26DAP	1.09061	0.819
51DAP/34DAP	0.86155	0.188
52DAP/51DAP	1.10615	0.492
53DAP/52DAP	1.04304	0.895
55DAP/53DAP	1.16051	0.733
57DAP/55DAP	1.4033	0.818
62DAP/57DAP	0.78291	0.028
68DAP/62DAP	0.82358	0.505
68DAP/14DAP	0.55891	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.52976	0.016

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.52669	0.055
Immature Eggplant/Mature Eggplant	1.66039	0.05
Ripe Pepper/Ripe Tomato	0.31713	0.224
Mature Eggplant/Ripe Tomato	0.35953	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.75112	N/A
12-2/M82	N/A	N/A
12-4/M82	0.90666	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	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.09203	N/A
4-3-2/M82	0.95881	0.698
4-3/M82	1.30732	1
5-3/M82	1.01998	1
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	0.9358	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.4647	0.337
IL7-5/WTpooled	0.22241	N/A
IL7-3/WTpooled	1.94121	1
IL12-4/WTpooled	0.92601	1
IL1-4/WTpooled	1.05635	1
WT/WTpooled	0.9627	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	1.46223	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.81572	0.868
DC3000/delta hrp 6h	1.29247	1
DC3000/delta hrp 12h	1.10052	1
DC3000/delta hrp 24h	1.16506	0.356

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.06929	1
DC3000 delta B/DC3000 delta AB	0.9057	0.189

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95975	1
Exp 36h	1.19461	0.693
Exp 60h	1.32828	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98665	1
Var 0h	0.87554	1
Var 12h I row2-row1	0.94208	0.705
Var 12h NI row2-row1	1.06219	1
Var 36h I row2-row1	1.02636	1
Var 36h NI row2-row1	1.00628	1
Var 60h I row2-row1	0.9425	0.285
Var 60h NI row2-row1	0.96828	1
Time course 0hI-0hNI	1.02087	0.852
Time course 12hI-12hNI	0.94792	0.436
Time course 36hI-36hNI	1.04575	0.166
Time course 60hI-60hNI	0.66412	0.006

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)	1.02258	0.748
transgenic ySAMdc/azygous control (breaker)	1.10113	1
transgenic ySAMdc/azygous control (red)	0.98056	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98324	0.5

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.03503	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89445	1
Manapal/WT (break)	0.86893	1
Manapal/WT (red)	0.85216	0.315