Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.17.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18977	0.67
27DAP/17DAP	0.8194	0.385
39DAP/27DAP	1.58244	0.077
41DAP/39DAP	0.93323	0.73
42DAP/41DAP	1.64133	0.122
43DAP/42DAP	1.56744	0.286
47DAP/43DAP	1.15539	0.569
52DAP/47DAP	0.72505	0.354
57DAP/52DAP	0.99684	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12734	0.366
17DAP/reference	0.8714	0.12
27DAP/reference	1.16203	0.299
39DAP/reference	0.81094	0.047
41DAP/reference	0.87732	0.201
42DAP/reference	1.06204	1
43DAP/reference	1.04344	0.73
47DAP/reference	1.22199	0.509
52DAP/reference	1.9482	0.031
57DAP/reference	1.733	0.049

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.82426	0.036
27DAP/17DAP	0.99225	0.919
39DAP/27DAP	2.1719	0.032
41DAP/39DAP	0.45535	0.013
42DAP/41DAP	1.2836	0.018
43DAP/42DAP	1.84823	0.014
47DAP/43DAP	0.85038	0.04
52DAP/47DAP	1.35919	0.19
57DAP/52DAP	0.98759	0.798
57DAP/7DAP	2.19947	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76282	0.115
17DAP/reference	0.66206	0.018
27DAP/reference	0.79182	0.018
39DAP/reference	1.1962	0.314
41DAP/reference	0.87726	0.203
42DAP/reference	1.34395	0.046
43DAP/reference	1.63716	0.045
47DAP/reference	1.52137	0.042
52DAP/reference	1.34304	0.046
57DAP/reference	1.81019	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8317	0.152
17DAP/reference	0.91359	0.245
27DAP/reference	0.88504	0.269
39DAP/reference	1.18126	0.061
41DAP/reference	1.5063	0.012
42DAP/reference	1.32616	0.068
43DAP/reference	0.79254	0.087
47DAP/reference	0.93655	0.221
52DAP/reference	1.22077	0.026
57DAP/reference	1.13981	0.398

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75229	0.05
17DAP/reference	0.92403	0.452
27DAP/reference	0.76614	0.043
39DAP/reference	1.14938	0.235
41DAP/reference	1.23116	0.074
42DAP/reference	2.16262	0.011
43DAP/reference	2.22865	0.006
47DAP/reference	1.34318	0.147
52DAP/reference	2.11468	0.115
57DAP/reference	1.89441	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97842	1
26DAP/20DAP	0.94545	1
34DAP/26DAP	1.00064	0.98
51DAP/34DAP	0.91019	0.66
52DAP/51DAP	1.14411	0.503
53DAP/52DAP	0.59606	0.066
55DAP/53DAP	0.80491	0.489
57DAP/55DAP	1.01385	0.97
62DAP/57DAP	1.11767	0.935
68DAP/62DAP	1.85812	0.193
68DAP/14DAP	2.94752	0.279

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.32582	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.5095	0.026
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.4621
Mature Eggplant/Ripe Tomato	0.57767	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.66014	0.742
1-1-2/M82	1.60147	1
12-2/M82	0.91987	0.955
12-4/M82	1.61113	1
1-3/M82	2.23157	0.479
2-1-1/M82	1.03362	1
2-1/M82	0.60504	0.322
2-6/M82	1.53298	0.329
3-2/M82	1.11197	0.463
4-1-1/M82	1.2027	1
4-1/M82	1.33524	1
4-3-2/M82	1.20777	1
4-3/M82	1.20571	1
5-3/M82	1.00045	1
6-2/M82	0.97566	0.473
6-3/M82	0.65482	0.982
7-1/M82	0.7279	0.44
7-2/M82	1.40296	0.385
9-3-2/M82	1.4894	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.85886	1
IL2-6/WTpooled	1.15306	0.427
IL7-5/WTpooled	0.75492	1
IL7-3/WTpooled	0.97162	1
IL12-4/WTpooled	1.06511	0.785
IL1-4/WTpooled	0.90748	0.476
WT/WTpooled	0.97251	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	0.8995	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02197	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.13667	1
DC3000/delta hrp 24h	0.57261	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.55989	0.023
DC3000 delta B/DC3000 delta AB	0.58933	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97973	1
Var 0h	1.05555	0.98
Var 12h I row2-row1	0.66529	0.344
Var 12h NI row2-row1	0.9598	0.82
Var 36h I row2-row1	0.99752	1
Var 36h NI row2-row1	1.51216	0.276
Var 60h I row2-row1	1.18365	0.543
Var 60h NI row2-row1	1.20103	0.904
Time course 0hI-0hNI	0.9647	0.808
Time course 12hI-12hNI	0.92743	0.41
Time course 36hI-36hNI	0.86405	0.108
Time course 60hI-60hNI	0.06412	0.005

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)	0.44464	0.246
transgenic ySAMdc/azygous control (breaker)	1.09602	1
transgenic ySAMdc/azygous control (red)	1.17711	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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)	N/A	N/A
Manapal/WT (break)	1.75685	0.183
Manapal/WT (red)	1.7619	0.137