Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.1.1.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.97563	0.033
27DAP/17DAP	0.98057	1
39DAP/27DAP	1.58503	0.097
41DAP/39DAP	0.58186	0.041
42DAP/41DAP	1.18199	0.852
43DAP/42DAP	0.96817	0.91
47DAP/43DAP	1.13061	0.555
52DAP/47DAP	0.9475	0.812
57DAP/52DAP	1.05264	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.68607	0.013
17DAP/reference	0.98491	0.737
27DAP/reference	0.80724	0.055
39DAP/reference	0.7257	0.042
41DAP/reference	0.74642	0.031
42DAP/reference	1.57245	0.001
43DAP/reference	0.87516	0.163
47DAP/reference	0.94744	0.242
52DAP/reference	0.92194	0.3
57DAP/reference	1.0015	0.701

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.708	0.036
27DAP/17DAP	1.16403	0.518
39DAP/27DAP	1.01771	1
41DAP/39DAP	1.37198	0.896
42DAP/41DAP	1.05281	0.887
43DAP/42DAP	0.84214	0.197
47DAP/43DAP	0.98852	0.933
52DAP/47DAP	1.04387	0.927
57DAP/52DAP	0.96181	0.657
57DAP/7DAP	1.21024	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.19773	0.035
17DAP/reference	1.24506	0.084
27DAP/reference	1.55891	0.015
39DAP/reference	1.37171	0.198
41DAP/reference	1.35519	0.018
42DAP/reference	1.47081	0.046
43DAP/reference	1.67252	0.008
47DAP/reference	1.73471	0.104
52DAP/reference	5.90703	0.008
57DAP/reference	3.57207	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.41988	0.058
17DAP/reference	1.80658	0.011
27DAP/reference	1.59868	0.045
39DAP/reference	1.15265	0.436
41DAP/reference	1.92813	0.005
42DAP/reference	1.81239	0.008
43DAP/reference	1.03304	0.706
47DAP/reference	1.33771	0.039
52DAP/reference	0.73788	0.004
57DAP/reference	1.05042	0.834

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.97975	0.015
17DAP/reference	1.14293	0.482
27DAP/reference	1.04153	0.871
39DAP/reference	1.39085	0.018
41DAP/reference	1.57466	0.029
42DAP/reference	1.77326	0.014
43DAP/reference	1.7412	0.011
47DAP/reference	0.77209	0.031
52DAP/reference	1.36712	0.075
57DAP/reference	1.39633	0.072

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.37504	0.966
26DAP/20DAP	1.38918	0.433
34DAP/26DAP	1.02797	1
51DAP/34DAP	0.97398	0.791
52DAP/51DAP	0.69175	0.151
53DAP/52DAP	1.08858	0.662
55DAP/53DAP	0.79966	0.035
57DAP/55DAP	1.00383	0.911
62DAP/57DAP	1.19298	0.678
68DAP/62DAP	1.36889	0.033
68DAP/14DAP	0.75225	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.5366	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.81921	0.274
Mature Green Tomato/Ripe Tomato	1.76202	0.053
Immature Eggplant/Mature Eggplant	0.93875	0.254
Ripe Pepper/Ripe Tomato	0.48941	0.224
Mature Eggplant/Ripe Tomato	0.74399	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.90189
12-2/M82	N/A	N/A
12-4/M82	1.29062	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.14997
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.93716
7-2/M82	N/A	N/A
9-3-2/M82	1.26892	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.04567	0.493
IL2-6/WTpooled	1.04158	0.659
IL7-5/WTpooled	1.06025	0.792
IL7-3/WTpooled	1.09256	1
IL12-4/WTpooled	1.03152	0.839
IL1-4/WTpooled	1.05393	1
WT/WTpooled	0.98083	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	1.19477	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11789	0.921
DC3000/delta hrp 6h	1.1321	1
DC3000/delta hrp 12h	1.00094	1
DC3000/delta hrp 24h	0.88102	0.323

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.00398	1
DC3000 delta B/DC3000 delta AB	1.00643	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.25441	1
Exp 36h	1.04464	1
Exp 60h	1.3315	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99578	1
Var 0h	0.52922	0.421
Var 12h I row2-row1	0.94107	0.705
Var 12h NI row2-row1	1.08568	1
Var 36h I row2-row1	1.1121	0.742
Var 36h NI row2-row1	1.15843	0.482
Var 60h I row2-row1	0.72429	0.582
Var 60h NI row2-row1	0.9517	1
Time course 0hI-0hNI	1.04828	0.833
Time course 12hI-12hNI	0.99237	0.994
Time course 36hI-36hNI	1.25947	0.013
Time course 60hI-60hNI	2.0614	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)	1.25166	0.297
transgenic ySAMdc/azygous control (breaker)	0.84379	0.49
transgenic ySAMdc/azygous control (red)	1.10604	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.17461	0.234

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.52533	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.20862	0.14
Manapal/WT (break)	1.0029	1
Manapal/WT (red)	N/A	N/A