Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.4.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.58858	0.048
27DAP/17DAP	0.97332	0.966
39DAP/27DAP	1.09884	0.841
41DAP/39DAP	0.7253	0.123
42DAP/41DAP	0.88298	1
43DAP/42DAP	1.09188	1
47DAP/43DAP	1.07007	0.733
52DAP/47DAP	0.89354	0.693
57DAP/52DAP	1.0273	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02113	0.928
17DAP/reference	1.05943	0.33
27DAP/reference	1.17912	0.01
39DAP/reference	1.17119	0.039
41DAP/reference	1.08637	0.054
42DAP/reference	1.07403	0.012
43DAP/reference	1.15448	0.012
47DAP/reference	1.21483	0.004
52DAP/reference	1.0481	0.607
57DAP/reference	1.09541	0.068

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.3768	0.04
27DAP/17DAP	1.08481	0.805
39DAP/27DAP	1.09232	0.56
41DAP/39DAP	1.18694	0.807
42DAP/41DAP	1.02329	1
43DAP/42DAP	0.8724	0.097
47DAP/43DAP	0.95353	0.734
52DAP/47DAP	1.04438	0.851
57DAP/52DAP	1.26369	0.197
57DAP/7DAP	1.26649	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31636	0.051
17DAP/reference	1.22437	0.019
27DAP/reference	1.30725	0.015
39DAP/reference	1.59752	0.006
41DAP/reference	1.24328	0.177
42DAP/reference	1.11234	0.828
43DAP/reference	1.36943	0.009
47DAP/reference	1.30981	0.033
52DAP/reference	1.274	0.011
57DAP/reference	1.39943	0.033

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02099	0.758
17DAP/reference	1.11195	0.061
27DAP/reference	1.19522	0.024
39DAP/reference	1.15151	0.063
41DAP/reference	1.07092	0.629
42DAP/reference	1.00854	0.723
43DAP/reference	1.06574	0.728
47DAP/reference	1.00028	0.695
52DAP/reference	1.22335	0.085
57DAP/reference	1.08482	0.146

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08317	0.397
17DAP/reference	1.0429	0.496
27DAP/reference	1.3084	0.034
39DAP/reference	1.42708	0.01
41DAP/reference	1.24852	0.023
42DAP/reference	1.20987	0.175
43DAP/reference	1.7263	0.038
47DAP/reference	1.16227	0.018
52DAP/reference	1.17111	0.463
57DAP/reference	1.19719	0.053

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02573	1
26DAP/20DAP	1.24175	0.504
34DAP/26DAP	1.06917	1
51DAP/34DAP	1.19384	0.154
52DAP/51DAP	0.7037	0.151
53DAP/52DAP	1.18646	0.24
55DAP/53DAP	0.89313	0.577
57DAP/55DAP	1.18948	0.543
62DAP/57DAP	0.92753	0.681
68DAP/62DAP	0.97266	0.834
68DAP/14DAP	1.45061	0.656

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	4.05186	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.99915	0.886
Mature Green Tomato/Ripe Tomato	1.48833	0.077
Immature Eggplant/Mature Eggplant	0.845	0.159
Ripe Pepper/Ripe Tomato	1.51054	1
Mature Eggplant/Ripe Tomato	1.16976	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06363	1
1-1-2/M82	1.03731	1
12-2/M82	0.87409	0.955
12-4/M82	1.13103	1
1-3/M82	1.47569
2-1-1/M82	0.9372
2-1/M82	N/A	N/A
2-6/M82	1.1068	1
3-2/M82	1.11553
4-1-1/M82	N/A	N/A
4-1/M82	1.65183	1
4-3-2/M82	1.04217	0.284
4-3/M82	0.81112	0.72
5-3/M82	1.10076	0.455
6-2/M82	N/A	N/A
6-3/M82	0.98032
7-1/M82	1.01966	1
7-2/M82	1.12305	1
9-3-2/M82	1.66465

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.98686	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.13257	1
IL12-4/WTpooled	0.99376	1
IL1-4/WTpooled	0.96622
WT/WTpooled	1.04805	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	0.92593	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09695	0.75
DC3000/delta hrp 6h	0.99009	0.95
DC3000/delta hrp 12h	0.98858	1
DC3000/delta hrp 24h	1.31187	0.057

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.48383	0.048
DC3000 delta B/DC3000 delta AB	1.67184	0.118

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.1836	1
Exp 36h	1.11671	1
Exp 60h	1.07571	1

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.84234
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.9076	0.32
transgenic ySAMdc/azygous control (breaker)	0.7449	0.173
transgenic ySAMdc/azygous control (red)	0.94327	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03301	0.448

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.04041	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.6425	0.172
Manapal/WT (break)	0.75529	0.299
Manapal/WT (red)	1.17867	0.222