Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.9.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91101	0.578
27DAP/17DAP	1.1744	0.847
39DAP/27DAP	0.84702	0.537
41DAP/39DAP	1.58119	0.282
42DAP/41DAP	1.08524	1
43DAP/42DAP	0.92657	0.858
47DAP/43DAP	0.9421	0.699
52DAP/47DAP	1.66663	0.24
57DAP/52DAP	1.169	0.771

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98506	0.63
17DAP/reference	1.03022	0.178
27DAP/reference	1.02996	0.684
39DAP/reference	1.02271	0.445
41DAP/reference	1.06174	0.079
42DAP/reference	0.96818	0.242
43DAP/reference	1.03035	0.596
47DAP/reference	0.93802	0.071
52DAP/reference	0.93873	0.172
57DAP/reference	0.82646	0.015

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90997	0.428
27DAP/17DAP	1.01009	0.969
39DAP/27DAP	1.04353	0.565
41DAP/39DAP	0.97652	0.98
42DAP/41DAP	1.03478	0.773
43DAP/42DAP	0.97905	0.684
47DAP/43DAP	0.99772	0.997
52DAP/47DAP	0.97524	0.893
57DAP/52DAP	1.02264	0.906
57DAP/7DAP	1.09344	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91137	0.072
17DAP/reference	0.95842	0.167
27DAP/reference	1.0028	0.974
39DAP/reference	0.90601	0.013
41DAP/reference	0.86112	0.029
42DAP/reference	0.76534	0.01
43DAP/reference	0.91068	0.121
47DAP/reference	0.8582	0.079
52DAP/reference	0.90968	0.115
57DAP/reference	0.91613	0.056

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05042	0.501
17DAP/reference	1.02765	0.892
27DAP/reference	0.99695	0.711
39DAP/reference	1.03214	0.956
41DAP/reference	0.95001	0.194
42DAP/reference	0.89111	0.023
43DAP/reference	1.08158	0.219
47DAP/reference	0.93439	0.033
52DAP/reference	1.04169	0.444
57DAP/reference	1.10423	0.229

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95932	0.119
17DAP/reference	1.02452	0.538
27DAP/reference	0.97513	0.257
39DAP/reference	0.92404	0.033
41DAP/reference	0.96338	0.459
42DAP/reference	0.85196	0.172
43DAP/reference	0.92042	0.305
47DAP/reference	0.90568	0.125
52DAP/reference	0.91753	0.22
57DAP/reference	0.61809	0.023

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99753	1
26DAP/20DAP	0.89098	0.317
34DAP/26DAP	0.93674	0.666
51DAP/34DAP	0.82512	0.076
52DAP/51DAP	0.9682	1
53DAP/52DAP	N/A	N/A
55DAP/53DAP	1.12555	0.319
57DAP/55DAP	1.01072	1
62DAP/57DAP	1.20956	0.098
68DAP/62DAP	0.88345	0.668
68DAP/14DAP	1.06	0.802

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.95024	0.322

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.34273	0.417
Mature Green Tomato/Ripe Tomato	0.89379	0.522
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96516	0.961
1-1-2/M82	0.98164	1
12-2/M82	1.08534	1
12-4/M82	0.95078	1
1-3/M82	1.0708	0.248
2-1-1/M82	1.19973	0.284
2-1/M82	1.27037
2-6/M82	1.03364	0.695
3-2/M82	0.90352	0.752
4-1-1/M82	0.95749	1
4-1/M82	0.83649	1
4-3-2/M82	0.85101	1
4-3/M82	0.8953	1
5-3/M82	1.08653	0.467
6-2/M82	0.96952	1
6-3/M82	1.0233	1
7-1/M82	1.03502	1
7-2/M82	1.35512
9-3-2/M82	0.93929	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	N/A	N/A
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	0.80614	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96467	1
DC3000/delta hrp 6h	1.06579	1
DC3000/delta hrp 12h	1.16673	1
DC3000/delta hrp 24h	1.08476	0.567

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.11216	0.441
DC3000 delta B/DC3000 delta AB	0.9552	0.543

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.0455	1
Exp 60h	1.22052	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9472	1
Var 0h	0.71246	1
Var 12h I row2-row1	1.16287	0.196
Var 12h NI row2-row1	0.95531	0.713
Var 36h I row2-row1	0.89897	0.805
Var 36h NI row2-row1	1.13327	1
Var 60h I row2-row1	1.31069	0.562
Var 60h NI row2-row1	1.23099	0.904
Time course 0hI-0hNI	1.10912	0.764
Time course 12hI-12hNI	1.01751	0.867
Time course 36hI-36hNI	1.02586	0.513
Time course 60hI-60hNI	1.22913	0.012

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)	0.78701	0.254
transgenic ySAMdc/azygous control (breaker)	0.87291	0.49
transgenic ySAMdc/azygous control (red)	1.01833	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02107	0.395

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.72998	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.94535	1
Manapal/WT (break)	0.84662	1
Manapal/WT (red)	1.0124	1