Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.7.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20955	0.838
27DAP/17DAP	1.55283	0.556
39DAP/27DAP	2.01144	0.029
41DAP/39DAP	1.119	0.708
42DAP/41DAP	1.08543	0.978
43DAP/42DAP	1.13904	0.956
47DAP/43DAP	1.49641	0.198
52DAP/47DAP	0.79957	0.525
57DAP/52DAP	1.80839	0.427

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.64382	0.024
17DAP/reference	0.80298	0.017
27DAP/reference	0.80675	0.026
39DAP/reference	1.44526	0.465
41DAP/reference	0.97539	0.667
42DAP/reference	1.60686	0.001
43DAP/reference	1.467	0.008
47DAP/reference	3.00757	0.001
52DAP/reference	1.35389	0.02
57DAP/reference	1.414	0.059

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8635	0.062
27DAP/17DAP	1.18245	0.518
39DAP/27DAP	1.04678	0.57
41DAP/39DAP	0.93191	0.599
42DAP/41DAP	0.91627	0.568
43DAP/42DAP	0.89444	0.172
47DAP/43DAP	0.94988	0.805
52DAP/47DAP	0.92059	0.304
57DAP/52DAP	1.21558	0.533
57DAP/7DAP	1.30801	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00304	0.758
17DAP/reference	0.88199	0.192
27DAP/reference	0.9945	0.656
39DAP/reference	0.95316	0.354
41DAP/reference	1.22419	0.113
42DAP/reference	1.24171	0.021
43DAP/reference	0.99427	0.608
47DAP/reference	1.13548	0.36
52DAP/reference	1.43067	0.011
57DAP/reference	2.65728	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.71311	0.014
17DAP/reference	0.76637	0.043
27DAP/reference	0.85431	0.111
39DAP/reference	0.87051	0.173
41DAP/reference	1.23331	0.025
42DAP/reference	1.13618	0.226
43DAP/reference	1.16638	0.899
47DAP/reference	3.77139	0.008
52DAP/reference	1.35982	0.008
57DAP/reference	2.1301	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04398	0.775
17DAP/reference	0.83381	0.118
27DAP/reference	1.22471	0.045
39DAP/reference	1.47244	0.013
41DAP/reference	1.23653	0.035
42DAP/reference	1.46175	0.018
43DAP/reference	1.4428	0.011
47DAP/reference	2.53598	0.005
52DAP/reference	2.33996	0.029
57DAP/reference	1.36801	0.141

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.14024	0.966
26DAP/20DAP	1.19852	0.39
34DAP/26DAP	1.12255	1
51DAP/34DAP	1.92501	0.047
52DAP/51DAP	1.01105	1
53DAP/52DAP	3.19149	0.204
55DAP/53DAP	3.59603	0.741
57DAP/55DAP	0.84407	0.3
62DAP/57DAP	2.273	0.004
68DAP/62DAP	0.831	0.543
68DAP/14DAP	1.2457	0.504

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.88418	0.224

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.07776	0.046
Mature Green Tomato/Ripe Tomato	0.48502	0.038
Immature Eggplant/Mature Eggplant	6.14125	0.05
Ripe Pepper/Ripe Tomato	2.62787	0.258
Mature Eggplant/Ripe Tomato	0.47105	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.79339	0.402
1-1-2/M82	1.60901	1
12-2/M82	1.03064	1
12-4/M82	0.95799	1
1-3/M82	4.1999	0.479
2-1-1/M82	0.99496	1
2-1/M82	1.09851	1
2-6/M82	1.39592	0.385
3-2/M82	1.02602
4-1-1/M82	0.8017
4-1/M82	N/A	N/A
4-3-2/M82	2.88658
4-3/M82	1.29648	1
5-3/M82	0.4965	0.419
6-2/M82	0.68888
6-3/M82	1.26447	1
7-1/M82	0.75847	0.509
7-2/M82	2.71107	0.385
9-3-2/M82	1.38321

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.82693
IL1-4/WTpooled	1.33233
WT/WTpooled	0.98246

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	1.31879	0.222

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00475	1
DC3000/delta hrp 6h	0.99477	0.95
DC3000/delta hrp 12h	1.01391	1
DC3000/delta hrp 24h	0.47653	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.14774	0.441
DC3000 delta B/DC3000 delta AB	1.46019	0.115

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03048	1
Exp 36h	0.91005	0.82
Exp 60h	0.73851	0.32

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97468	1
Var 0h	0.6591	1
Var 12h I row2-row1	0.92053	0.627
Var 12h NI row2-row1	1.34562	0.649
Var 36h I row2-row1	0.96504	1
Var 36h NI row2-row1	1.14801	1
Var 60h I row2-row1	0.60026	0.287
Var 60h NI row2-row1	0.78794	0.329
Time course 0hI-0hNI	0.99372	1
Time course 12hI-12hNI	1.16862	0.287
Time course 36hI-36hNI	2.1678	0.004
Time course 60hI-60hNI	6.00866	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)	0.58583	0.314
transgenic ySAMdc/azygous control (breaker)	0.95498	1
transgenic ySAMdc/azygous control (red)	1.19588	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.66489	0.047

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.97901	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.77263	0.093
Manapal/WT (break)	5.0247	0.14
Manapal/WT (red)	1.97257	0.133