Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.7.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08821	0.964
27DAP/17DAP	1.12595	0.845
39DAP/27DAP	1.03824	0.956
41DAP/39DAP	0.87264	0.499
42DAP/41DAP	0.90707	1
43DAP/42DAP	0.93805	0.786
47DAP/43DAP	0.91217	0.696
52DAP/47DAP	0.98755	0.89
57DAP/52DAP	0.98224	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.101	0.097
17DAP/reference	1.03428	0.282
27DAP/reference	0.97315	0.339
39DAP/reference	0.97735	0.565
41DAP/reference	0.99003	0.814
42DAP/reference	1.00149	0.707
43DAP/reference	0.99188	0.785
47DAP/reference	0.96851	0.224
52DAP/reference	0.9508	0.25
57DAP/reference	0.89381	0.023

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89929	0.26
27DAP/17DAP	0.97086	0.887
39DAP/27DAP	1.04185	0.685
41DAP/39DAP	1.10288	0.641
42DAP/41DAP	1.00182	0.924
43DAP/42DAP	1.11216	0.273
47DAP/43DAP	1.03742	0.873
52DAP/47DAP	0.92405	0.702
57DAP/52DAP	0.79167	0.177
57DAP/7DAP	1.49938

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09821	0.28
17DAP/reference	1.0945	0.361
27DAP/reference	0.93251	0.283
39DAP/reference	1.12929	0.634
41DAP/reference	1.12321	0.56
42DAP/reference	0.94392	0.436
43DAP/reference	0.89208	0.292
47DAP/reference	1.02403	0.837
52DAP/reference	1.22978	0.105
57DAP/reference	1.06791	0.654

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04799	0.712
17DAP/reference	1.10631	0.037
27DAP/reference	1.12708	0.283
39DAP/reference	1.10796	0.225
41DAP/reference	0.8377	0.103
42DAP/reference	0.9297	0.169
43DAP/reference	1.25024	0.047
47DAP/reference	0.97706	0.39
52DAP/reference	1.05256	0.259
57DAP/reference	1.06921	0.334

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26101	0.053
17DAP/reference	1.25448	0.085
27DAP/reference	1.11788	0.111
39DAP/reference	1.01097	0.935
41DAP/reference	1.23202	0.129
42DAP/reference	1.05096	0.73
43DAP/reference	1.34381	0.131
47DAP/reference	0.93996	0.12
52DAP/reference	0.97017	0.637
57DAP/reference	0.89094	0.028

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9158	0.961
26DAP/20DAP	1.22477	0.962
34DAP/26DAP	1.06445	1
51DAP/34DAP	1.00184	0.917
52DAP/51DAP	1.19172	0.722
53DAP/52DAP	1.03404	0.944
55DAP/53DAP	1.06609	0.842
57DAP/55DAP	0.98129	0.821
62DAP/57DAP	0.80584
68DAP/62DAP	0.90729
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.00825	0.043

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.12071	0.666
Mature Green Tomato/Ripe Tomato	1.98843	0.058
Immature Eggplant/Mature Eggplant	0.88401	0.176
Ripe Pepper/Ripe Tomato	1.58106	0.256
Mature Eggplant/Ripe Tomato	1.79159	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92506	0.613
1-1-2/M82	N/A	N/A
12-2/M82	0.74224
12-4/M82	1.08833	0.655
1-3/M82	0.99791
2-1-1/M82	0.97753	1
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	N/A	N/A
4-3-2/M82	1.24247
4-3/M82	N/A	N/A
5-3/M82	1.18652	0.496
6-2/M82	1.05743
6-3/M82	0.81511
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	0.89765	1
IL2-6/WTpooled	1.0203	1
IL7-5/WTpooled	1.48369	0.792
IL7-3/WTpooled	0.96484	1
IL12-4/WTpooled	0.85232	0.71
IL1-4/WTpooled	0.86741	0.476
WT/WTpooled	0.97179	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	1.07308	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92705	1
DC3000/delta hrp 6h	1.05109	1
DC3000/delta hrp 12h	1.03709	1
DC3000/delta hrp 24h	0.8396	0.14

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.68432	0.052
DC3000 delta B/DC3000 delta AB	0.72693	0.03

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.15198	1
Exp 36h	0.8249	0.699
Exp 60h	0.80834	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03317	1
Var 0h	1.25292	0.782
Var 12h I row2-row1	0.86042	0.418
Var 12h NI row2-row1	0.87811	0.427
Var 36h I row2-row1	0.97779	0.805
Var 36h NI row2-row1	0.88847	0.645
Var 60h I row2-row1	1.03888	1
Var 60h NI row2-row1	0.97562	0.516
Time course 0hI-0hNI	1.00392	1
Time course 12hI-12hNI	0.94261	0.522
Time course 36hI-36hNI	0.8995	0.089
Time course 60hI-60hNI	0.66259	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)	0.89184	0.299
transgenic ySAMdc/azygous control (breaker)	1.12103	1
transgenic ySAMdc/azygous control (red)	1.12609	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03381	0.135

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95182	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.33177	0.105
Manapal/WT (break)	1.20278	1
Manapal/WT (red)	1.01867	1