Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.3.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88133	0.464
27DAP/17DAP	1.10293	0.872
39DAP/27DAP	1.04968	1
41DAP/39DAP	0.95443	0.771
42DAP/41DAP	1.11346	0.92
43DAP/42DAP	1.09378	1
47DAP/43DAP	0.99972	0.949
52DAP/47DAP	1.09971	0.96
57DAP/52DAP	1.10134	0.993

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11553	0.5
17DAP/reference	1.25858	0.014
27DAP/reference	0.94109	0.642
39DAP/reference	0.81398	0.404
41DAP/reference	1.27708	0.085
42DAP/reference	1.56348
43DAP/reference	3.6867
47DAP/reference	1.20856
52DAP/reference	1.01662	0.709
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.26923	0.154
27DAP/17DAP	1.16636	0.645
39DAP/27DAP	1.11929	0.57
41DAP/39DAP	0.96123	0.893
42DAP/41DAP	1.03459	0.892
43DAP/42DAP	1.41625	0.021
47DAP/43DAP	1.0426	0.95
52DAP/47DAP	1.10945	0.689
57DAP/52DAP	1.32206	0.133
57DAP/7DAP	1.06037	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.59971	0.066
17DAP/reference	0.68469	0.044
27DAP/reference	0.72851	0.03
39DAP/reference	0.95492	0.354
41DAP/reference	0.86115	0.073
42DAP/reference	1.23473	0.405
43DAP/reference	1.22642	0.325
47DAP/reference	1.0832	0.822
52DAP/reference	0.93942	0.254
57DAP/reference	0.84657	0.061

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99005	0.786
17DAP/reference	1.11997	0.264
27DAP/reference	1.09134	0.23
39DAP/reference	1.0677	0.543
41DAP/reference	1.04774	0.766
42DAP/reference	1.07787	0.794
43DAP/reference	0.98929	0.681
47DAP/reference	1.00651	1
52DAP/reference	1.0577	0.629
57DAP/reference	2.29266	0.398

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.67924	0.038
17DAP/reference	0.8355	0.275
27DAP/reference	0.62068	0.03
39DAP/reference	0.66855	0.008
41DAP/reference	0.80119	0.031
42DAP/reference	1.63289	0.011
43DAP/reference	1.55764	0.01
47DAP/reference	1.32979	0.032
52DAP/reference	1.48093	0.046
57DAP/reference	1.12352	0.298

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91966	0.997
26DAP/20DAP	2.564	0.099
34DAP/26DAP	0.92699	0.783
51DAP/34DAP	1.19725	0.251
52DAP/51DAP	1.13819	0.704
53DAP/52DAP	0.83665	0.445
55DAP/53DAP	0.92744	0.709
57DAP/55DAP	1.12012	0.955
62DAP/57DAP	1.24106	0.257
68DAP/62DAP	0.90792	0.769
68DAP/14DAP	0.91249	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.09944	0.908

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.34095	0.017
Immature Eggplant/Mature Eggplant	1.69431	0.165
Ripe Pepper/Ripe Tomato	0.08575	0.224
Mature Eggplant/Ripe Tomato	0.1301	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.10314	1
1-1-2/M82	1.10559	1
12-2/M82	0.95789	0.955
12-4/M82	1.02214	1
1-3/M82	1.44737	0.26
2-1-1/M82	0.90896	0.565
2-1/M82	0.33393
2-6/M82	1.09518	0.695
3-2/M82	1.11466	0.84
4-1-1/M82	1.01813	1
4-1/M82	N/A	N/A
4-3-2/M82	1.16482	1
4-3/M82	1.20641	1
5-3/M82	0.84036	0.642
6-2/M82	N/A	N/A
6-3/M82	0.95227	1
7-1/M82	0.87245	0.803
7-2/M82	0.94454	1
9-3-2/M82	0.88166

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.09735	0.365
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.46156	0.792
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.7145	0.71
IL1-4/WTpooled	1.1195	1
WT/WTpooled	0.91083	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	1.11662	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94276	1
DC3000/delta hrp 6h	1.1568	1
DC3000/delta hrp 12h	1.22501	1
DC3000/delta hrp 24h	1.18662	0.158

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	1.05414	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07969	0.254
Exp 36h	1.42043	0.489
Exp 60h	1.22558	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01875	1
Var 0h	0.63512	1
Var 12h I row2-row1	0.97469
Var 12h NI row2-row1	0.89863	0.82
Var 36h I row2-row1	1.18699	0.908
Var 36h NI row2-row1	1.22785	1
Var 60h I row2-row1	1.21589	0.483
Var 60h NI row2-row1	0.958	1
Time course 0hI-0hNI	0.92733	0.39
Time course 12hI-12hNI	0.92437	0.47
Time course 36hI-36hNI	0.97599	0.559
Time course 60hI-60hNI	0.46099	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)	0.93571	0.32
transgenic ySAMdc/azygous control (breaker)	0.61523	0.131
transgenic ySAMdc/azygous control (red)	0.99579	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9641	0.471

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.56683	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.15378	0.14
Manapal/WT (break)	1.7557	0.381
Manapal/WT (red)	1.05775	1