Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.9.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90853	0.568
27DAP/17DAP	0.95157	0.911
39DAP/27DAP	0.91321	0.608
41DAP/39DAP	0.99975	0.92
42DAP/41DAP	1.1932	0.873
43DAP/42DAP	0.86479	0.77
47DAP/43DAP	1.24069	0.595
52DAP/47DAP	0.97745	0.818
57DAP/52DAP	1.0901	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11469	0.334
17DAP/reference	1.14006	0.048
27DAP/reference	1.04882	0.75
39DAP/reference	1.16211	0.149
41DAP/reference	1.15226	0.05
42DAP/reference	0.9231	0.139
43DAP/reference	1.1034	0.495
47DAP/reference	0.87026	0.106
52DAP/reference	0.9911	0.618
57DAP/reference	1.02442	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99623	0.782
27DAP/17DAP	1.26051	0.35
39DAP/27DAP	1.13304	0.636
41DAP/39DAP	0.77003	0.072
42DAP/41DAP	1.2638	0.478
43DAP/42DAP	1.22055	0.122
47DAP/43DAP	1.01231	1
52DAP/47DAP	1.39896	0.474
57DAP/52DAP	1.00152	0.726
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0381	0.961
17DAP/reference	1.12682	0.574
27DAP/reference	0.96265	0.402
39DAP/reference	1.03163	0.865
41DAP/reference	1.15326	0.43
42DAP/reference	1.24899	0.405
43DAP/reference	1.2947	0.037
47DAP/reference	0.94881	0.293
52DAP/reference	0.93768	0.304
57DAP/reference	1.02655	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13178	0.308
17DAP/reference	1.27873	0.484
27DAP/reference	0.96175	0.438
39DAP/reference	1.14633	0.463
41DAP/reference	0.98511	0.531
42DAP/reference	0.83012	0.073
43DAP/reference	1.12269	0.641
47DAP/reference	0.88404	0.113
52DAP/reference	1.1606	0.057
57DAP/reference	1.29087	0.08

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04816	0.882
17DAP/reference	1.25719	0.088
27DAP/reference	1.20973	0.037
39DAP/reference	1.03545	0.792
41DAP/reference	1.08461	0.537
42DAP/reference	1.03701	0.943
43DAP/reference	0.94039	0.384
47DAP/reference	1.03895	0.966
52DAP/reference	0.85738	0.204
57DAP/reference	0.81722	0.124

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.43294	0.207
26DAP/20DAP	1.38043	0.642
34DAP/26DAP	1.05567	1
51DAP/34DAP	1.54082	0.483
52DAP/51DAP	1.15833	0.722
53DAP/52DAP	1.02042	1
55DAP/53DAP	0.77241	0.376
57DAP/55DAP	1.04339	0.986
62DAP/57DAP	0.86887	0.681
68DAP/62DAP	0.63779	0.263
68DAP/14DAP	0.82844	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.57999	0.663

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.22335	0.209
Immature Eggplant/Mature Eggplant	0.12188
Ripe Pepper/Ripe Tomato	0.44491	0.293
Mature Eggplant/Ripe Tomato	0.44026	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00468	1
1-1-2/M82	0.97366	1
12-2/M82	1.04711
12-4/M82	1.2285
1-3/M82	0.62648
2-1-1/M82	0.91722
2-1/M82	N/A	N/A
2-6/M82	0.97981
3-2/M82	N/A	N/A
4-1-1/M82	0.97689
4-1/M82	0.96743
4-3-2/M82	1.06482
4-3/M82	N/A	N/A
5-3/M82	0.94384	1
6-2/M82	0.94347
6-3/M82	0.88383	1
7-1/M82	N/A	N/A
7-2/M82	0.95821	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.57071
IL2-6/WTpooled	1.01476	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.00511	1
IL12-4/WTpooled	0.91773	1
IL1-4/WTpooled	0.88643
WT/WTpooled	0.9434	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	0.86513	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94703	1
DC3000/delta hrp 6h	0.94646	0.95
DC3000/delta hrp 12h	0.96314	1
DC3000/delta hrp 24h	1.06395	0.483

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.61978	0.171
DC3000 delta B/DC3000 delta AB	1.04431	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94297	0.265
Exp 36h	N/A	N/A
Exp 60h	0.88033	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00146
Var 0h	1.0491	0.98
Var 12h I row2-row1	0.8334	0.627
Var 12h NI row2-row1	4.51108	1
Var 36h I row2-row1	0.67544	0.805
Var 36h NI row2-row1	0.64978	0.852
Var 60h I row2-row1	1.16755	1
Var 60h NI row2-row1	0.85689	0.904
Time course 0hI-0hNI	1.06074	0.852
Time course 12hI-12hNI	0.91913	0.402
Time course 36hI-36hNI	0.93962	0.23
Time course 60hI-60hNI	0.7343	0.007

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)	1.09037	0.347
transgenic ySAMdc/azygous control (breaker)	0.99861	1
transgenic ySAMdc/azygous control (red)	1.39834	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.8955	0.052

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.02566	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.72274	0.084
Manapal/WT (break)	1.21753	1
Manapal/WT (red)	1.31892	0.137