Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.7.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18447	0.443
27DAP/17DAP	0.53497	0.045
39DAP/27DAP	0.82001	0.512
41DAP/39DAP	0.61998	0.063
42DAP/41DAP	0.78685	0.774
43DAP/42DAP	1.13989	1
47DAP/43DAP	0.45724	0.051
52DAP/47DAP	1.11914	0.873
57DAP/52DAP	0.97011	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77436	0.068
17DAP/reference	0.84284	0.05
27DAP/reference	0.8157	0.027
39DAP/reference	0.82407	0.146
41DAP/reference	0.81645	0.026
42DAP/reference	0.80049	0.001
43DAP/reference	0.97436	0.611
47DAP/reference	0.83669	0.001
52DAP/reference	0.79264	0.067
57DAP/reference	0.91384	0.138

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.82558	0.036
27DAP/17DAP	0.70574	0.187
39DAP/27DAP	0.41283	0.031
41DAP/39DAP	1.34159	0.119
42DAP/41DAP	0.85022	0.178
43DAP/42DAP	0.70902	0.022
47DAP/43DAP	1.03562	0.93
52DAP/47DAP	1.10732	0.756
57DAP/52DAP	0.92285	0.546
57DAP/7DAP	0.47784	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13247	0.235
17DAP/reference	0.8868	0.018
27DAP/reference	0.58605	0.01
39DAP/reference	0.5535	0.011
41DAP/reference	0.43028	0.009
42DAP/reference	0.39825	0.01
43DAP/reference	0.36759	0.009
47DAP/reference	0.50899	0.05
52DAP/reference	0.41876	0.009
57DAP/reference	0.43143	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74201	0.01
17DAP/reference	0.77071	0.017
27DAP/reference	0.82162	0.079
39DAP/reference	0.68283	0.009
41DAP/reference	0.83815	0.044
42DAP/reference	0.80667	0.042
43DAP/reference	0.51935	0.003
47DAP/reference	0.72502	0.008
52DAP/reference	0.63728	0.004
57DAP/reference	0.62033	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.31724	0.015
17DAP/reference	1.84853	0.151
27DAP/reference	1.45616	0.033
39DAP/reference	1.20084	0.163
41DAP/reference	0.82661	0.046
42DAP/reference	0.64331	0.018
43DAP/reference	0.72162	0.022
47DAP/reference	0.65843	0.004
52DAP/reference	0.58598	0.047
57DAP/reference	1.0303	1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98291	1
26DAP/20DAP	1.02892	1
34DAP/26DAP	0.8076	0.165
51DAP/34DAP	0.49404	0.049
52DAP/51DAP	1.08782	0.349
53DAP/52DAP	0.76158	0.15
55DAP/53DAP	0.9105	0.102
57DAP/55DAP	1.00064	0.968
62DAP/57DAP	1.52447	0.723
68DAP/62DAP	0.926	0.609
68DAP/14DAP	0.99545	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.54518	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.53527	0.058
Mature Green Tomato/Ripe Tomato	22.1667	0.015
Immature Eggplant/Mature Eggplant	0.43946	0.057
Ripe Pepper/Ripe Tomato	4.09232	0.258
Mature Eggplant/Ripe Tomato	17.5253	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98756	1
1-1-2/M82	0.98646
12-2/M82	1.28204
12-4/M82	1.08225	0.344
1-3/M82	0.74493	0.378
2-1-1/M82	1.34184
2-1/M82	N/A	N/A
2-6/M82	1.24073	0.505
3-2/M82	0.81079
4-1-1/M82	0.88602	0.985
4-1/M82	1.0678
4-3-2/M82	1.18952
4-3/M82	0.86866	1
5-3/M82	0.98244	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.89783	0.796
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.93254
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.2661	1
IL12-4/WTpooled	0.93703	1
IL1-4/WTpooled	0.94597	1
WT/WTpooled	0.97915	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	1.01034	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96403	1
DC3000/delta hrp 6h	0.95258	0.95
DC3000/delta hrp 12h	0.99824	1
DC3000/delta hrp 24h	1.02258	0.76

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.96501	0.691
DC3000 delta B/DC3000 delta AB	0.67769	0.117

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	0.97678	1
Var 0h	1.0998	1
Var 12h I row2-row1	1.09299	0.58
Var 12h NI row2-row1	1.00411	1
Var 36h I row2-row1	1.13308	1
Var 36h NI row2-row1	0.89858	0.347
Var 60h I row2-row1	1.25289	0.543
Var 60h NI row2-row1	1.06528	0.904
Time course 0hI-0hNI	1.00546	1
Time course 12hI-12hNI	0.98179	0.897
Time course 36hI-36hNI	1.02979	0.722
Time course 60hI-60hNI	0.65585	0.026

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)	1.20861	0.541
transgenic ySAMdc/azygous control (breaker)	0.93505	0.251
transgenic ySAMdc/azygous control (red)	0.79459	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.6766	0.099

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.64301	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	5.02444	0.09
Manapal/WT (break)	3.15177	0.123
Manapal/WT (red)	1.70779	1