Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.7.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.39725	0.094
27DAP/17DAP	1.42599	1
39DAP/27DAP	5.1947	0.048
41DAP/39DAP	1.25079	0.437
42DAP/41DAP	2.05734	0.024
43DAP/42DAP	0.75388	0.497
47DAP/43DAP	0.5403	0.077
52DAP/47DAP	1.16967	0.89
57DAP/52DAP	1.1082	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95479	0.39
17DAP/reference	1.00576	0.957
27DAP/reference	1.03965	0.637
39DAP/reference	1.07312	0.593
41DAP/reference	1.00215	0.814
42DAP/reference	1.043	0.931
43DAP/reference	0.97185	0.708
47DAP/reference	0.99179	0.602
52DAP/reference	0.85384	0.102
57DAP/reference	1.11436	0.084

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	3.05988	0.036
27DAP/17DAP	0.4551	0.121
39DAP/27DAP	3.57927	0.04
41DAP/39DAP	0.60825	0.013
42DAP/41DAP	1.29732	0.134
43DAP/42DAP	1.20397	0.034
47DAP/43DAP	0.53766	0.008
52DAP/47DAP	0.92729	0.79
57DAP/52DAP	0.75319	0.215
57DAP/7DAP	1.05561	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.71196	0.076
17DAP/reference	0.55389	0.013
27DAP/reference	0.94797	0.248
39DAP/reference	1.55661	0.016
41DAP/reference	0.64398	0.033
42DAP/reference	1.04631	1
43DAP/reference	0.77638	0.069
47DAP/reference	1.17087	0.458
52DAP/reference	0.47385	0.01
57DAP/reference	0.37186	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04773	0.626
17DAP/reference	1.0368	0.999
27DAP/reference	1.10581	0.618
39DAP/reference	0.86697	0.202
41DAP/reference	0.98571	0.505
42DAP/reference	0.97232	0.482
43DAP/reference	1.24164	0.327
47DAP/reference	1.08662	0.482
52DAP/reference	1.00336	0.619
57DAP/reference	1.08355	0.771

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.59001	0.04
17DAP/reference	0.88758	0.381
27DAP/reference	0.61231	0.039
39DAP/reference	0.84065	0.101
41DAP/reference	1.35823	0.022
42DAP/reference	1.70761	0.026
43DAP/reference	1.21857	0.59
47DAP/reference	0.96937	0.465
52DAP/reference	1.39645	0.908
57DAP/reference	0.82101	0.12

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12201	0.678
26DAP/20DAP	0.94255	1
34DAP/26DAP	1.34683	0.819
51DAP/34DAP	0.86924	0.376
52DAP/51DAP	0.85346	1
53DAP/52DAP	0.89814	0.649
55DAP/53DAP	1.10132	0.782
57DAP/55DAP	1.64533	0.061
62DAP/57DAP	0.75894	0.028
68DAP/62DAP	1.18361	0.754
68DAP/14DAP	1.4251

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	14.6951	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.95164
Mature Green Tomato/Ripe Tomato	1.13912	0.399
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.32861	0.256
Mature Eggplant/Ripe Tomato	1.70373	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.7286
12-2/M82	1.25905
12-4/M82	0.8366	0.619
1-3/M82	N/A	N/A
2-1-1/M82	0.9471	1
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.25796
4-1-1/M82	1.42905	1
4-1/M82	N/A	N/A
4-3-2/M82	2.23122
4-3/M82	1.53901	1
5-3/M82	0.96916	1
6-2/M82	3.5364
6-3/M82	1.99692
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	2.05387

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.00971	1
IL2-6/WTpooled	1.15662	0.788
IL7-5/WTpooled	0.96816	1
IL7-3/WTpooled	0.62204	0.31
IL12-4/WTpooled	0.84807	0.71
IL1-4/WTpooled	0.8867	0.699
WT/WTpooled	0.9733	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	1.30277	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.17757	0.692
DC3000/delta hrp 6h	1.12356	1
DC3000/delta hrp 12h	0.95378	1
DC3000/delta hrp 24h	0.81031	0.079

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.7548	0.042
DC3000 delta B/DC3000 delta AB	2.25124	0.027

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.80913	0.328
Exp 36h	0.79179	0.489
Exp 60h	1.02724	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00508	1
Var 0h	0.98138	1
Var 12h I row2-row1	1.19328	0.324
Var 12h NI row2-row1	1.21641	0.34
Var 36h I row2-row1	1.25374	0.742
Var 36h NI row2-row1	0.94951	0.706
Var 60h I row2-row1	0.92874	0.832
Var 60h NI row2-row1	0.8793	0.63
Time course 0hI-0hNI	1.01044	1
Time course 12hI-12hNI	1.14313	0.44
Time course 36hI-36hNI	2.15842	0.004
Time course 60hI-60hNI	1.97332	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)	1.08046	0.272
transgenic ySAMdc/azygous control (breaker)	1.12045	1
transgenic ySAMdc/azygous control (red)	1.04384	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9823	0.201

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.09318	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.06828	0.307
Manapal/WT (break)	1.37035	0.123
Manapal/WT (red)	2.31501	0.164