Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.9.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22416	0.561
27DAP/17DAP	1.00578	0.996
39DAP/27DAP	1.19453	0.649
41DAP/39DAP	1.02529	0.88
42DAP/41DAP	1.22353	0.773
43DAP/42DAP	1.31541	0.722
47DAP/43DAP	1.3532	0.527
52DAP/47DAP	0.86718	0.662
57DAP/52DAP	0.93213	0.92

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01999	1
17DAP/reference	0.85368	0.091
27DAP/reference	0.95509	0.595
39DAP/reference	0.78711	0.03
41DAP/reference	0.85338	0.018
42DAP/reference	0.94495	0.188
43DAP/reference	0.89937	0.103
47DAP/reference	0.90422	0.077
52DAP/reference	1.05604	0.663
57DAP/reference	1.05122	0.6

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02048	0.975
27DAP/17DAP	1.05636	0.863
39DAP/27DAP	0.91839	0.371
41DAP/39DAP	0.91063	0.645
42DAP/41DAP	1.034	1
43DAP/42DAP	0.93448	0.383
47DAP/43DAP	0.99679	0.989
52DAP/47DAP	1.1694	0.558
57DAP/52DAP	1.04596	0.951
57DAP/7DAP	1.9834	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20644	0.418
17DAP/reference	1.18806	0.896
27DAP/reference	1.12356	0.371
39DAP/reference	1.15509	0.57
41DAP/reference	1.43929	0.46
42DAP/reference	1.02043	0.751
43DAP/reference	1.06059	0.788
47DAP/reference	0.99463	1
52DAP/reference	1.06629	0.401
57DAP/reference	0.94772	0.28

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91768	0.342
17DAP/reference	0.8593	0.106
27DAP/reference	1.22444	0.735
39DAP/reference	0.97545	0.509
41DAP/reference	1.00754	0.57
42DAP/reference	0.88645	0.212
43DAP/reference	0.86187	0.285
47DAP/reference	0.83048	0.06
52DAP/reference	0.93543	0.327
57DAP/reference	0.84155	0.023

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.61693
17DAP/reference	1.14928	0.545
27DAP/reference	1.13655	0.298
39DAP/reference	1.15989	0.014
41DAP/reference	1.20325	0.115
42DAP/reference	0.64901
43DAP/reference	0.93019
47DAP/reference	0.88413	0.231
52DAP/reference	0.91342	0.464
57DAP/reference	0.92294	0.516

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.23201	0.966
26DAP/20DAP	1.06408	0.793
34DAP/26DAP	1.08032	1
51DAP/34DAP	0.99859	0.927
52DAP/51DAP	0.96849	1
53DAP/52DAP	0.70964	0.087
55DAP/53DAP	0.89629	0.577
57DAP/55DAP	1.02654	0.96
62DAP/57DAP	1.34446	0.393
68DAP/62DAP	1.07716	0.582
68DAP/14DAP	1.50058	0.504

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.7576	0.122

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.88237
Mature Green Tomato/Ripe Tomato	2.97146	0.015
Immature Eggplant/Mature Eggplant	0.51213	0.062
Ripe Pepper/Ripe Tomato	0.94254
Mature Eggplant/Ripe Tomato	7.13792

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.06607
12-2/M82	N/A	N/A
12-4/M82	1.25936	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	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.00184
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.05142	0.493
IL2-6/WTpooled	1.15438
IL7-5/WTpooled	0.80816	1
IL7-3/WTpooled	1.22086	1
IL12-4/WTpooled	0.93049	1
IL1-4/WTpooled	0.96932
WT/WTpooled	1.04165	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	0.82858	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.8709	0.734
DC3000/delta hrp 6h	0.82481	0.95
DC3000/delta hrp 12h	0.89683	1
DC3000/delta hrp 24h	1.08415	0.75

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.02519	1
DC3000 delta B/DC3000 delta AB	0.97029	0.826

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07037	1
Exp 36h	0.65669	0.406
Exp 60h	0.75042	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	1.23848	1
Var 0h	1.16485	0.98
Var 12h I row2-row1	1.06942	0.283
Var 12h NI row2-row1	1.02542	1
Var 36h I row2-row1	1.03092	0.305
Var 36h NI row2-row1	1.12403	1
Var 60h I row2-row1	0.96368	0.439
Var 60h NI row2-row1	1.07731	0.904
Time course 0hI-0hNI	0.94297	0.629
Time course 12hI-12hNI	0.94135	0.54
Time course 36hI-36hNI	0.74491	0.053
Time course 60hI-60hNI	0.40786	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)	1.0536	0.612
transgenic ySAMdc/azygous control (breaker)	0.87972	0.173
transgenic ySAMdc/azygous control (red)	1.21246	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9391	0.083

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.57958	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.5659	0.084
Manapal/WT (break)	1.1784	1
Manapal/WT (red)	1.0454	1