Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-1.1.4.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.40083	0.073
27DAP/17DAP	1.29767	0.809
39DAP/27DAP	0.78863	0.41
41DAP/39DAP	1.18799	0.67
42DAP/41DAP	1.06764	1
43DAP/42DAP	1.11736	0.993
47DAP/43DAP	1.17445	0.609
52DAP/47DAP	0.86063	0.618
57DAP/52DAP	1.00256	0.988

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83185	0.077
17DAP/reference	0.92427	0.097
27DAP/reference	1.06628	0.782
39DAP/reference	1.17842	0.091
41DAP/reference	1.14268	0.034
42DAP/reference	1.61877	0.001
43DAP/reference	1.7003	0.01
47DAP/reference	2.80753	0.001
52DAP/reference	2.06706	0.008
57DAP/reference	1.81747	0.017

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9693	0.679
27DAP/17DAP	1.09767	0.771
39DAP/27DAP	1.18356	N/A
41DAP/39DAP	0.57995	0.013
42DAP/41DAP	2.46656	0.002
43DAP/42DAP	2.82353	0.013
47DAP/43DAP	0.94574	0.75
52DAP/47DAP	1.16116	0.718
57DAP/52DAP	1.0686	0.971
57DAP/7DAP	2.34581	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98678	0.613
17DAP/reference	0.91295	0.039
27DAP/reference	0.96277	0.325
39DAP/reference	0.95366	0.146
41DAP/reference	1.19511	0.024
42DAP/reference	0.96631	0.169
43DAP/reference	0.90098	0.115
47DAP/reference	1.12579	0.804
52DAP/reference	1.14286	0.159
57DAP/reference	1.08949	0.536

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91001	0.087
17DAP/reference	0.79627	0.012
27DAP/reference	1.03957	1
39DAP/reference	1.25779	0.073
41DAP/reference	1.05859	0.893
42DAP/reference	1.10772	0.38
43DAP/reference	1.05451	0.957
47DAP/reference	1.26364	0.022
52DAP/reference	1.04738	0.702
57DAP/reference	1.04742	0.848

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8104	0.104
17DAP/reference	0.98454	0.727
27DAP/reference	0.83665	0.036
39DAP/reference	0.88392	0.017
41DAP/reference	1.00364	0.826
42DAP/reference	1.12846	0.802
43DAP/reference	1.21718	0.555
47DAP/reference	1.92722	0.007
52DAP/reference	1.23416	0.649
57DAP/reference	1.59451	0.068

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.31811	0.586
26DAP/20DAP	0.75368	0.223
34DAP/26DAP	1.31547	0.154
51DAP/34DAP	0.92776	0.587
52DAP/51DAP	0.98218	1
53DAP/52DAP	1.51044	0.033
55DAP/53DAP	1.08903	0.589
57DAP/55DAP	0.97602	0.875
62DAP/57DAP	0.32863	0.003
68DAP/62DAP	1.9207	0.073
68DAP/14DAP	1.82596	0.087

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.38477	0.7

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.50539	0.168
Mature Green Tomato/Ripe Tomato	2.61659	0.017
Immature Eggplant/Mature Eggplant	6.24742	0.05
Ripe Pepper/Ripe Tomato	0.08774	0.224
Mature Eggplant/Ripe Tomato	0.06275	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96326	N/A
1-1-2/M82	1.11778	1
12-2/M82	1.1637	N/A
12-4/M82	1.14928	1
1-3/M82	0.75214	N/A
2-1-1/M82	1.0313	N/A
2-1/M82	N/A	N/A
2-6/M82	1.21138	0.505
3-2/M82	0.83409	0.752
4-1-1/M82	N/A	N/A
4-1/M82	1.29846	0.466
4-3-2/M82	0.73244	0.487
4-3/M82	0.76744	N/A
5-3/M82	0.94249	0.49
6-2/M82	N/A	N/A
6-3/M82	1.2501	1
7-1/M82	1.06827	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.03244	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.71238	1
IL2-6/WTpooled	0.73715	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.78602	1
IL12-4/WTpooled	1.09175	0.516
IL1-4/WTpooled	1.00873	N/A
WT/WTpooled	0.99026	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	1.09502	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98913	1
DC3000/delta hrp 6h	0.9125	0.95
DC3000/delta hrp 12h	1.18091	1
DC3000/delta hrp 24h	1.85988	0.212

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.85759	0.724
DC3000 delta B/DC3000 delta AB	1.11044	0.55

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.76499	1
Exp 36h	1.46338	0.693
Exp 60h	1.5273	0.221

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0526	1
Var 0h	0.89817	0.936
Var 12h I row2-row1	1.06842	0.736
Var 12h NI row2-row1	1.03654	1
Var 36h I row2-row1	0.87154	0.575
Var 36h NI row2-row1	1.15255	0.482
Var 60h I row2-row1	1.29351	0.543
Var 60h NI row2-row1	1.03553	0.904
Time course 0hI-0hNI	0.98175	0.93
Time course 12hI-12hNI	0.92916	0.687
Time course 36hI-36hNI	0.75112	0.023
Time course 60hI-60hNI	0.4613	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)	1.41916	0.272
transgenic ySAMdc/azygous control (breaker)	0.4852	0.125
transgenic ySAMdc/azygous control (red)	0.69438	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05487	0.096

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.49813	0.172
Manapal/WT (break)	1.00551	1
Manapal/WT (red)	0.77828	0.216