Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.16.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85173	0.373
27DAP/17DAP	0.86172	0.655
39DAP/27DAP	1.53492	0.115
41DAP/39DAP	0.69248	0.087
42DAP/41DAP	0.8235	0.774
43DAP/42DAP	1.14606	0.875
47DAP/43DAP	0.463	0.049
52DAP/47DAP	1.01998	0.908
57DAP/52DAP	1.06048	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03977	0.928
17DAP/reference	1.14549	0.089
27DAP/reference	0.988	0.741
39DAP/reference	1.12879	0.032
41DAP/reference	1.18307	0.067
42DAP/reference	0.92994	0.091
43DAP/reference	1.0489	0.596
47DAP/reference	0.91534	0.127
52DAP/reference	0.81773	0.096
57DAP/reference	0.82568	0.035

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87504	0.219
27DAP/17DAP	1.01181	0.98
39DAP/27DAP	0.80096	0.06
41DAP/39DAP	1.06366	1
42DAP/41DAP	0.93607	0.508
43DAP/42DAP	0.87037	0.037
47DAP/43DAP	0.98014	0.909
52DAP/47DAP	0.60923	0.058
57DAP/52DAP	0.93075	0.605
57DAP/7DAP	0.38203	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.52407	0.03
17DAP/reference	1.95879	0.006
27DAP/reference	1.74175	0.01
39DAP/reference	1.81236	0.006
41DAP/reference	1.67237	0.012
42DAP/reference	1.71509	0.007
43DAP/reference	2.16336	0.006
47DAP/reference	1.22607	0.647
52DAP/reference	1.6799	0.011
57DAP/reference	1.62572	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0109	0.993
17DAP/reference	0.98641	0.626
27DAP/reference	0.92595	0.212
39DAP/reference	0.83726	0.089
41DAP/reference	0.96424	0.357
42DAP/reference	0.7978	0.016
43DAP/reference	1.05008	1
47DAP/reference	0.9682	0.379
52DAP/reference	0.95436	0.203
57DAP/reference	1.34918	0.039

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.50052	0.024
17DAP/reference	1.19039	0.511
27DAP/reference	2.01602	0.015
39DAP/reference	1.85133	0.014
41DAP/reference	1.71737	0.01
42DAP/reference	1.42934	0.204
43DAP/reference	1.58907	0.209
47DAP/reference	0.9314	0.249
52DAP/reference	1.69589	0.113
57DAP/reference	1.05913	0.372

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05912	0.966
26DAP/20DAP	2.8872	0.097
34DAP/26DAP	0.60583	0.148
51DAP/34DAP	1.00933	0.924
52DAP/51DAP	0.84483	1
53DAP/52DAP	0.93613	0.703
55DAP/53DAP	0.75054	0.176
57DAP/55DAP	1.01568	0.872
62DAP/57DAP	1.01547	0.994
68DAP/62DAP	1.09724	1
68DAP/14DAP	0.74136	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	4.265	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.62863	1
Mature Green Tomato/Ripe Tomato	1.9622	0.015
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.98613	1
Mature Eggplant/Ripe Tomato	0.79113	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.15272	0.526
1-1-2/M82	1.22611
12-2/M82	1.22377
12-4/M82	0.87292	0.33
1-3/M82	0.94576
2-1-1/M82	0.66011
2-1/M82	1.09753	1
2-6/M82	1.0474	0.395
3-2/M82	0.70781
4-1-1/M82	0.88178
4-1/M82	0.362
4-3-2/M82	1.20479	1
4-3/M82	0.61719	0.72
5-3/M82	0.97108	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.01061	1
7-2/M82	0.94188	0.881
9-3-2/M82	1.4359	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.00284	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.1463	0.362
IL12-4/WTpooled	1.17407	0.538
IL1-4/WTpooled	0.9479
WT/WTpooled	1.08986	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	1.08589	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02914	0.921
DC3000/delta hrp 6h	1.00817	0.95
DC3000/delta hrp 12h	1.14827	1
DC3000/delta hrp 24h	0.99463	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.24104	0.081
DC3000 delta B/DC3000 delta AB	1.39532	0.141

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88466	1
Exp 36h	0.87898	0.589
Exp 60h	0.96076	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00318	1
Var 0h	0.67482	0.933
Var 12h I row2-row1	0.90295	0.418
Var 12h NI row2-row1	1.03302	1
Var 36h I row2-row1	1.15999	0.601
Var 36h NI row2-row1	1.0395	1
Var 60h I row2-row1	0.86864	0.439
Var 60h NI row2-row1	0.90925	0.756
Time course 0hI-0hNI	1.04971	0.764
Time course 12hI-12hNI	1.03311	0.773
Time course 36hI-36hNI	1.328	0.007
Time course 60hI-60hNI	1.43482	0.011

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)	1.01126	0.571
transgenic ySAMdc/azygous control (breaker)	1.08477	1
transgenic ySAMdc/azygous control (red)	1.11589	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9748	0.444

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.86452	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92071	1
Manapal/WT (break)	0.93737	1
Manapal/WT (red)	0.80676	0.315