Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.12.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.73922	0.249
27DAP/17DAP	1.11912	0.92
39DAP/27DAP	0.95313	0.663
41DAP/39DAP	0.93445	0.726
42DAP/41DAP	1.03841	1
43DAP/42DAP	0.91707	0.851
47DAP/43DAP	0.93693	0.746
52DAP/47DAP	1.31861	0.676
57DAP/52DAP	0.92506	0.833

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.40565	0.05
17DAP/reference	1.1641	0.22
27DAP/reference	1.76221	0.587
39DAP/reference	1.04284	0.734
41DAP/reference	1.29169	0.054
42DAP/reference	1.23182	0.006
43DAP/reference	1.02739	0.678
47DAP/reference	1.15974	0.075
52DAP/reference	1.05447	0.633
57DAP/reference	0.94813	0.358

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14903	0.558
27DAP/17DAP	1.00421	0.943
39DAP/27DAP	1.01664	0.832
41DAP/39DAP	0.92343	0.861
42DAP/41DAP	1.06074	0.991
43DAP/42DAP	1.02874	0.83
47DAP/43DAP	1.12684	0.572
52DAP/47DAP	0.71292	0.096
57DAP/52DAP	0.83568	0.137
57DAP/7DAP	1.40024	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.5215	0.054
17DAP/reference	1.49085	0.01
27DAP/reference	1.31598	0.035
39DAP/reference	0.96863	0.411
41DAP/reference	0.9832	0.589
42DAP/reference	0.93566	0.304
43DAP/reference	1.12922	0.672
47DAP/reference	1.2113	0.353
52DAP/reference	1.22876	0.066
57DAP/reference	1.18741	0.033

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02565	0.93
17DAP/reference	1.77857	0.024
27DAP/reference	1.61999	0.028
39DAP/reference	1.18543	0.141
41DAP/reference	1.49079	0.006
42DAP/reference	1.48274	0.011
43DAP/reference	1.07372	1
47DAP/reference	1.32869	0.025
52DAP/reference	1.153	0.194
57DAP/reference	1.48593	0.021

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23244	0.138
17DAP/reference	1.37658	0.092
27DAP/reference	1.19635	0.051
39DAP/reference	1.34872	0.064
41DAP/reference	1.29901	0.008
42DAP/reference	1.51859	0.024
43DAP/reference	1.6778	0.015
47DAP/reference	1.12574	0.704
52DAP/reference	1.25627	0.928
57DAP/reference	1.29646	0.049

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	N/A	N/A
26DAP/20DAP	0.7854	0.512
34DAP/26DAP	1.02126	0.991
51DAP/34DAP	1.37069	0.118
52DAP/51DAP	0.88112	1
53DAP/52DAP	1.13427	0.458
55DAP/53DAP	0.91078	0.735
57DAP/55DAP	1.13804	0.407
62DAP/57DAP	0.95489	0.871
68DAP/62DAP	0.98156	0.641
68DAP/14DAP	0.8335	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.76714	0.129

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.02575	0.485
Ripe Pepper/Ripe Tomato	0.93996
Mature Eggplant/Ripe Tomato	2.39362

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	1.05245
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	N/A	N/A
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	N/A	N/A
IL2-6/WTpooled	0.89991	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.04821
IL12-4/WTpooled	1.0844	0.557
IL1-4/WTpooled	0.95747	1
WT/WTpooled	0.88015	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	0.97717	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00998	1
DC3000/delta hrp 6h	1.24578	1
DC3000/delta hrp 12h	1.17344	1
DC3000/delta hrp 24h	1.02013	0.821

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.87777	0.497

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.35901	1
Exp 36h	0.83755	0.661
Exp 60h	0.99767	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99903	1
Var 0h	1.1385	0.98
Var 12h I row2-row1	0.95877	0.77
Var 12h NI row2-row1	0.93925	0.438
Var 36h I row2-row1	0.93878	0.805
Var 36h NI row2-row1	1.07537	1
Var 60h I row2-row1	0.98252	0.952
Var 60h NI row2-row1	1.11098	0.904
Time course 0hI-0hNI	0.97908	0.892
Time course 12hI-12hNI	0.95146	0.484
Time course 36hI-36hNI	0.88954	0.078
Time course 60hI-60hNI	0.46467	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)	1.0228	0.921
transgenic ySAMdc/azygous control (breaker)	0.88546	0.49
transgenic ySAMdc/azygous control (red)	0.96072	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.20752	0.036

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.97128	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.13767	0.307
Manapal/WT (break)	0.99918	1
Manapal/WT (red)	1.03147	1