Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.7.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.31721	0.281
27DAP/17DAP	0.52273	0.027
39DAP/27DAP	1.21679	0.542
41DAP/39DAP	0.59506	0.047
42DAP/41DAP	1.11198	1
43DAP/42DAP	1.05812	1
47DAP/43DAP	0.70182	0.185
52DAP/47DAP	0.83179	0.502
57DAP/52DAP	1.05662	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74584	0.115
17DAP/reference	0.69033	0.035
27DAP/reference	0.60889	0.013
39DAP/reference	0.6143	0.026
41DAP/reference	0.4797	0.009
42DAP/reference	0.52089	0.001
43DAP/reference	0.34158	0.013
47DAP/reference	0.2104	0.001
52DAP/reference	0.22342	0.012
57DAP/reference	0.27509	0.006

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.65283	0.067
27DAP/17DAP	0.84211	0.684
39DAP/27DAP	0.33305	0.028
41DAP/39DAP	1.5425	0.393
42DAP/41DAP	0.89307	0.56
43DAP/42DAP	0.69832	0.034
47DAP/43DAP	1.01266	1
52DAP/47DAP	1.00115	0.97
57DAP/52DAP	1.01282	0.913
57DAP/7DAP	0.29129	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20498	0.201
17DAP/reference	0.9664	0.447
27DAP/reference	0.7277	0.045
39DAP/reference	0.7157	0.012
41DAP/reference	0.67448	0.021
42DAP/reference	0.63421	0.012
43DAP/reference	0.53231	0.012
47DAP/reference	0.58348	0.044
52DAP/reference	0.57287	0.019
57DAP/reference	0.4566	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.45624	0.007
17DAP/reference	0.79096	0.143
27DAP/reference	0.92714	0.352
39DAP/reference	0.7209	0.016
41DAP/reference	0.59051	0.013
42DAP/reference	0.71131	0.028
43DAP/reference	0.47759	0.017
47DAP/reference	0.71506	0.027
52DAP/reference	0.39648	0.004
57DAP/reference	0.39514	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.58367	0.016
17DAP/reference	1.98219	0.203
27DAP/reference	1.62224	0.029
39DAP/reference	1.25462	0.108
41DAP/reference	0.87269	0.107
42DAP/reference	0.6752	0.059
43DAP/reference	0.69101	0.025
47DAP/reference	0.24234	0.004
52DAP/reference	0.4293	0.072
57DAP/reference	0.96636	0.483

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94684	1
26DAP/20DAP	1.1817	0.604
34DAP/26DAP	0.81278	0.261
51DAP/34DAP	0.56742	0.059
52DAP/51DAP	0.97854	1
53DAP/52DAP	0.81762	0.212
55DAP/53DAP	1.01367	0.964
57DAP/55DAP	0.92427	0.652
62DAP/57DAP	1.07407	0.833
68DAP/62DAP	1.6525	0.121
68DAP/14DAP	0.76789	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.77425	0.038

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	13.986	0.089
Mature Green Tomato/Ripe Tomato	4.44789	0.016
Immature Eggplant/Mature Eggplant	0.80219	0.077
Ripe Pepper/Ripe Tomato	13.0761	1
Mature Eggplant/Ripe Tomato	19.3553	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96932	0.961
1-1-2/M82	1.14667	1
12-2/M82	0.64208	0.639
12-4/M82	1.14018	1
1-3/M82	1.0011	1
2-1-1/M82	N/A	N/A
2-1/M82	0.73185
2-6/M82	1.18213	0.505
3-2/M82	0.9947	1
4-1-1/M82	1.35823	1
4-1/M82	2.28291	0.225
4-3-2/M82	1.20502
4-3/M82	0.89642	1
5-3/M82	2.56465	0.572
6-2/M82	1.38062	1
6-3/M82	0.94769	1
7-1/M82	1.43484	0.598
7-2/M82	1.30201	0.385
9-3-2/M82	1.71226	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.32523	0.277
IL2-6/WTpooled	1.35081	0.456
IL7-5/WTpooled	1.41539	0.792
IL7-3/WTpooled	1.02597	1
IL12-4/WTpooled	1.26239	0.503
IL1-4/WTpooled	0.95446	0.834
WT/WTpooled	0.83707	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	1.16048	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9128
DC3000/delta hrp 6h	0.98674	0.95
DC3000/delta hrp 12h	0.80126	1
DC3000/delta hrp 24h	0.9799	0.924

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.88822	0.273
DC3000 delta B/DC3000 delta AB	0.68876	0.045

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0359	1
Exp 36h	0.90253	0.661
Exp 60h	0.86886	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00063	1
Var 0h	0.78319	0.933
Var 12h I row2-row1	0.93069	0.357
Var 12h NI row2-row1	0.9055	0.494
Var 36h I row2-row1	1.06312	1
Var 36h NI row2-row1	1.13821	1
Var 60h I row2-row1	1.3015	0.562
Var 60h NI row2-row1	1.03141	1
Time course 0hI-0hNI	0.95149	0.577
Time course 12hI-12hNI	1.01705	0.773
Time course 36hI-36hNI	0.97771	0.476
Time course 60hI-60hNI	0.4757	0.015

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)	1.18435	0.511
transgenic ySAMdc/azygous control (breaker)	2.26609	0.172
transgenic ySAMdc/azygous control (red)	1.90825	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.46472	0.072

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.34244	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	11.0464	0.083
Manapal/WT (break)	6.16119	0.14
Manapal/WT (red)	2.07996	1