Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.9.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.69754	0.068
27DAP/17DAP	1.01204	0.93
39DAP/27DAP	0.75199	0.435
41DAP/39DAP	1.0286	0.904
42DAP/41DAP	1.49252	0.493
43DAP/42DAP	1.29185	0.772
47DAP/43DAP	1.02652	0.965
52DAP/47DAP	0.79921	0.459
57DAP/52DAP	1.47046	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93844	0.412
17DAP/reference	0.82592	0.069
27DAP/reference	0.87952	0.349
39DAP/reference	0.85358	0.136
41DAP/reference	0.80969	0.031
42DAP/reference	0.85095	0.052
43DAP/reference	0.94525	0.519
47DAP/reference	0.97831	0.503
52DAP/reference	0.6697	0.05
57DAP/reference	0.95846	0.456

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94455	0.509
27DAP/17DAP	0.87211	0.508
39DAP/27DAP	0.80865	0.06
41DAP/39DAP	0.9831	0.997
42DAP/41DAP	1.19127	0.241
43DAP/42DAP	0.89525	0.256
47DAP/43DAP	0.98861	0.961
52DAP/47DAP	0.96385	0.876
57DAP/52DAP	1.23479	0.338
57DAP/7DAP	0.59999

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76663	0.071
17DAP/reference	0.90048	0.044
27DAP/reference	0.86298	0.058
39DAP/reference	0.86608	0.012
41DAP/reference	0.81705	0.009
42DAP/reference	0.8854	0.022
43DAP/reference	0.7826	0.021
47DAP/reference	0.78245	0.128
52DAP/reference	0.76613	0.023
57DAP/reference	0.76889	0.012

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10752	0.23
17DAP/reference	0.9525	0.474
27DAP/reference	0.90622	0.327
39DAP/reference	0.80163	0.076
41DAP/reference	0.807	0.045
42DAP/reference	0.70736	0.018
43DAP/reference	1.015	0.721
47DAP/reference	0.87438	0.027
52DAP/reference	0.79515	0.047
57DAP/reference	0.90234	0.278

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93687	0.158
17DAP/reference	0.87348	0.292
27DAP/reference	0.91763	0.286
39DAP/reference	0.87192	0.043
41DAP/reference	0.87221	0.107
42DAP/reference	0.90117	0.018
43DAP/reference	0.88513	0.035
47DAP/reference	1.13878	0.461
52DAP/reference	0.7441	0.068
57DAP/reference	0.96174	0.468

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97821	1
26DAP/20DAP	1.1014	0.798
34DAP/26DAP	1.0376	1
51DAP/34DAP	1.20582	0.089
52DAP/51DAP	0.99031	1
53DAP/52DAP	0.82042	0.221
55DAP/53DAP	0.83332	0.462
57DAP/55DAP	1.33445	0.906
62DAP/57DAP	1.17177	0.868
68DAP/62DAP	0.8591	0.747
68DAP/14DAP	1.13548	0.762

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.65841	0.025

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.59132
Mature Green Tomato/Ripe Tomato	1.76106	0.523
Immature Eggplant/Mature Eggplant	1.42621	0.321
Ripe Pepper/Ripe Tomato	2.02535	1
Mature Eggplant/Ripe Tomato	2.41664	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.08956	1
1-1-2/M82	0.88538	1
12-2/M82	0.94968
12-4/M82	0.70828	0.298
1-3/M82	N/A	N/A
2-1-1/M82	1.21983	0.764
2-1/M82	0.65763	0.519
2-6/M82	1.15843	0.505
3-2/M82	0.93953	0.455
4-1-1/M82	1.05287	1
4-1/M82	N/A	N/A
4-3-2/M82	1.45811
4-3/M82	1.13359	1
5-3/M82	0.92745	1
6-2/M82	1.21501
6-3/M82	1.12166	1
7-1/M82	0.86477	1
7-2/M82	1.18562	1
9-3-2/M82	1.28321	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.28099	0.277
IL2-6/WTpooled	0.98927	1
IL7-5/WTpooled	1.02595	1
IL7-3/WTpooled	1.03272	1
IL12-4/WTpooled	1.0665	0.503
IL1-4/WTpooled	0.9959	1
WT/WTpooled	1.00083	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	0.95324	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.87677	0.599
DC3000/delta hrp 6h	0.97929	0.95
DC3000/delta hrp 12h	0.91414	1
DC3000/delta hrp 24h	0.48931	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.80883	0.033
DC3000 delta B/DC3000 delta AB	0.72388	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.7417	1
Exp 36h	0.73175	0.456
Exp 60h	0.7479	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00257	1
Var 0h	1.09507	0.98
Var 12h I row2-row1	0.85876	0.514
Var 12h NI row2-row1	1.00944	1
Var 36h I row2-row1	1.19445	0.908
Var 36h NI row2-row1	1.41701	1
Var 60h I row2-row1	0.91301	0.374
Var 60h NI row2-row1	1.05378	1
Time course 0hI-0hNI	1.00699	1
Time course 12hI-12hNI	1.02092	0.82
Time course 36hI-36hNI	0.90816	0.125
Time course 60hI-60hNI	0.27869	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)	1.28332	0.268
transgenic ySAMdc/azygous control (breaker)	0.93224	1
transgenic ySAMdc/azygous control (red)	1.07434	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.78081	0.115

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.38977	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.02787	0.084
Manapal/WT (break)	1.93905	0.14
Manapal/WT (red)	1.2945	0.164