Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.9.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0055	1
27DAP/17DAP	0.84888	0.615
39DAP/27DAP	1.26814	0.318
41DAP/39DAP	1.14717	0.376
42DAP/41DAP	1.09412	0.958
43DAP/42DAP	0.75176	0.522
47DAP/43DAP	0.70929	0.221
52DAP/47DAP	1.4657	0.456
57DAP/52DAP	0.63083	0.622

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14355	0.366
17DAP/reference	1.04288	0.143
27DAP/reference	0.99375	0.797
39DAP/reference	1.0405	0.352
41DAP/reference	1.09211	0.158
42DAP/reference	0.94172	0.176
43DAP/reference	1.02229	0.787
47DAP/reference	0.89852	0.035
52DAP/reference	0.83326	0.058
57DAP/reference	0.83219	0.051

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81223	0.103
27DAP/17DAP	1.23368	0.22
39DAP/27DAP	0.71544	0.035
41DAP/39DAP	1.09787	0.79
42DAP/41DAP	0.88404	0.3
43DAP/42DAP	0.91624	0.137
47DAP/43DAP	0.90638	0.339
52DAP/47DAP	1.13902	0.619
57DAP/52DAP	0.89865	0.451
57DAP/7DAP	0.78861	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9261	0.246
17DAP/reference	0.89418	0.02
27DAP/reference	0.87175	0.02
39DAP/reference	0.74654	0.011
41DAP/reference	0.71689	0.019
42DAP/reference	0.72109	0.023
43DAP/reference	0.74558	0.025
47DAP/reference	0.90603	0.168
52DAP/reference	0.70021	0.013
57DAP/reference	0.68274	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24037	0.041
17DAP/reference	1.2315	0.012
27DAP/reference	1.15753	0.283
39DAP/reference	1.01157	1
41DAP/reference	0.94317	0.133
42DAP/reference	0.83583	0.012
43DAP/reference	1.32934	0.031
47DAP/reference	0.87498	0.062
52DAP/reference	1.19083	0.018
57DAP/reference	1.21176	0.131

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94694	0.23
17DAP/reference	1.03227	0.665
27DAP/reference	0.87468	0.081
39DAP/reference	0.83877	0.035
41DAP/reference	0.87552	0.055
42DAP/reference	0.91655	0.445
43DAP/reference	0.71105	0.023
47DAP/reference	1.03088	0.877
52DAP/reference	1.09579	0.946
57DAP/reference	0.79355	0.048

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.106	0.966
26DAP/20DAP	0.99136	1
34DAP/26DAP	0.88065	0.472
51DAP/34DAP	1.08528	0.706
52DAP/51DAP	0.99647	1
53DAP/52DAP	1.22846	0.712
55DAP/53DAP	1.06194	0.834
57DAP/55DAP	1.18277	0.407
62DAP/57DAP	1.10475	0.35
68DAP/62DAP	0.8368	0.314
68DAP/14DAP	0.61467	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.62057	0.026

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.80323
Mature Green Tomato/Ripe Tomato	2.25941	0.017
Immature Eggplant/Mature Eggplant	1.12939	0.23
Ripe Pepper/Ripe Tomato	2.30511	0.256
Mature Eggplant/Ripe Tomato	8.58207	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.89963	0.907
1-1-2/M82	N/A	N/A
12-2/M82	1.04324	1
12-4/M82	0.91442	0.619
1-3/M82	0.73107	0.286
2-1-1/M82	1.04599
2-1/M82	N/A	N/A
2-6/M82	0.96426	1
3-2/M82	0.91898
4-1-1/M82	1.09955	1
4-1/M82	N/A	N/A
4-3-2/M82	1.06802
4-3/M82	0.89528
5-3/M82	0.99984	1
6-2/M82	0.78407
6-3/M82	1.00951	1
7-1/M82	N/A	N/A
7-2/M82	1.08124	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.0637
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	0.88166	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96773	1
DC3000/delta hrp 6h	0.87454	0.95
DC3000/delta hrp 12h	1.05078	1
DC3000/delta hrp 24h	0.99646	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.67495	0.041
DC3000 delta B/DC3000 delta AB	0.85173	0.236

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.83116	0.328
Exp 36h	0.90107	0.699
Exp 60h	0.95435	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00698	1
Var 0h	0.93388	1
Var 12h I row2-row1	0.98657	1
Var 12h NI row2-row1	0.88764	0.546
Var 36h I row2-row1	0.95695	1
Var 36h NI row2-row1	0.99027	0.852
Var 60h I row2-row1	1.52173	0.562
Var 60h NI row2-row1	1.22785	0.904
Time course 0hI-0hNI	1.09286	0.63
Time course 12hI-12hNI	0.97558	0.782
Time course 36hI-36hNI	0.84762	0.023
Time course 60hI-60hNI	0.73908	0.047

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)	0.91354	0.454
transgenic ySAMdc/azygous control (breaker)	0.8731	0.15
transgenic ySAMdc/azygous control (red)	0.98122	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99158	0.362

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.84292	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89591	1
Manapal/WT (break)	1.11795	1
Manapal/WT (red)	1.09845	1