Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.12.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05418	0.863
27DAP/17DAP	1.02089	1
39DAP/27DAP	0.86453	0.549
41DAP/39DAP	3.19925	0.112
42DAP/41DAP	3.31809	0.034
43DAP/42DAP	9.45367	0.019
47DAP/43DAP	1.56571	0.377
52DAP/47DAP	0.37127	0.034
57DAP/52DAP	0.698	0.708

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.18586	0.024
17DAP/reference	0.22135	0.006
27DAP/reference	0.23288	0.005
39DAP/reference	0.59318	0.03
41DAP/reference	0.34327	0.008
42DAP/reference	2.03866	0.013
43DAP/reference	13.0744	0.006
47DAP/reference	12.1585	0.001
52DAP/reference	1.84897	0.108
57DAP/reference	3.18879	0.136

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.73168	0.153
27DAP/17DAP	1.14423	0.694
39DAP/27DAP	1.16323	0.603
41DAP/39DAP	0.97706	0.986
42DAP/41DAP	2.52564	0.039
43DAP/42DAP	6.0488	0.013
47DAP/43DAP	1.55037	0.025
52DAP/47DAP	1.78673	0.159
57DAP/52DAP	0.43907	0.047
57DAP/7DAP	1.6031	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85404	0.296
17DAP/reference	1.27887	0.006
27DAP/reference	1.57881	0.008
39DAP/reference	1.39482	0.006
41DAP/reference	1.18469	0.46
42DAP/reference	1.23874	0.046
43DAP/reference	1.06863	0.672
47DAP/reference	0.63996	0.128
52DAP/reference	1.32424	0.015
57DAP/reference	1.3108	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.38686	0.009
17DAP/reference	0.20945	0.003
27DAP/reference	0.20232	0.005
39DAP/reference	0.16814	0.007
41DAP/reference	0.22111	0.005
42DAP/reference	0.36964	0.013
43DAP/reference	0.70578	0.084
47DAP/reference	0.38836	0.01
52DAP/reference	0.16467	0.003
57DAP/reference	0.19809	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85769	0.29
17DAP/reference	0.76046	0.286
27DAP/reference	1.14533	0.871
39DAP/reference	1.06585	0.693
41DAP/reference	1.01252	0.754
42DAP/reference	1.75507	0.016
43DAP/reference	3.91443	0.038
47DAP/reference	12.3211	0.004
52DAP/reference	2.37647	0.22
57DAP/reference	0.72175	0.078

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04124	0.966
26DAP/20DAP	1.0191	1
34DAP/26DAP	1.16388	1
51DAP/34DAP	0.89653	0.508
52DAP/51DAP	1.34057	0.596
53DAP/52DAP	1.08325	0.91
55DAP/53DAP	1.32947	0.104
57DAP/55DAP	0.96958	0.76
62DAP/57DAP	0.40185	0.016
68DAP/62DAP	1.661	0.926
68DAP/14DAP	0.98576	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.19769	0.821

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.04316	0.017
Immature Eggplant/Mature Eggplant	0.99234	1
Ripe Pepper/Ripe Tomato	0.04577	0.224
Mature Eggplant/Ripe Tomato	0.04104	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	2.88438	0.526
1-1-2/M82	3.00522	1
12-2/M82	0.995	1
12-4/M82	4.34945	1
1-3/M82	3.18814	0.277
2-1-1/M82	1.22315	0.689
2-1/M82	0.56728	0.325
2-6/M82	1.99794	0.425
3-2/M82	1.46738	0.84
4-1-1/M82	2.11826	0.998
4-1/M82	11.4227	0.853
4-3-2/M82	2.04336	0.241
4-3/M82	1.2605	1
5-3/M82	0.91551	0.642
6-2/M82	3.6445	0.235
6-3/M82	1.10523	1
7-1/M82	0.96453	0.803
7-2/M82	1.61277	0.385
9-3-2/M82	2.80511	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.7612
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	1.06571

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02232	0.921
DC3000/delta hrp 6h	0.98853	0.95
DC3000/delta hrp 12h	1.10619	1
DC3000/delta hrp 24h	1.07912	0.422

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.45355
DC3000 delta B/DC3000 delta AB	0.95502

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.26548	1
Exp 36h	1.13254	1
Exp 60h	0.85774	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01255	1
Var 0h	2.91368	0.936
Var 12h I row2-row1	0.73661	0.363
Var 12h NI row2-row1	0.80556	0.494
Var 36h I row2-row1	1.15732	1
Var 36h NI row2-row1	1.39109	1
Var 60h I row2-row1	0.96169	1
Var 60h NI row2-row1	1.18923	1
Time course 0hI-0hNI	1.04353	0.852
Time course 12hI-12hNI	0.91927	0.426
Time course 36hI-36hNI	0.83203	0.074
Time course 60hI-60hNI	0.38467	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)	1.07268	0.325
transgenic ySAMdc/azygous control (breaker)	0.73163	0.251
transgenic ySAMdc/azygous control (red)	0.96257	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98652	0.418

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.24505	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.90452	1
Manapal/WT (break)	1.04359	1
Manapal/WT (red)	0.74097	0.274