Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.19.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97904	0.743
27DAP/17DAP	1.14224	0.859
39DAP/27DAP	0.93722	0.641
41DAP/39DAP	1.5107	0.63
42DAP/41DAP	1.06925	1
43DAP/42DAP	0.91766	0.841
47DAP/43DAP	0.91358	0.687
52DAP/47DAP	1.31106	0.535
57DAP/52DAP	0.8657	0.85

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.998	0.756
17DAP/reference	0.92367	0.298
27DAP/reference	1.05691	0.981
39DAP/reference	1.11975	0.465
41DAP/reference	1.17601	0.552
42DAP/reference	1.60323	0.001
43DAP/reference	1.11755	0.495
47DAP/reference	1.46226	0.003
52DAP/reference	1.3869	0.019
57DAP/reference	1.03891	0.762

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13908	0.278
27DAP/17DAP	1.00955	1
39DAP/27DAP	0.91794	0.482
41DAP/39DAP	1.17891	0.427
42DAP/41DAP	0.92514	0.451
43DAP/42DAP	0.85756	0.082
47DAP/43DAP	1.07999	0.61
52DAP/47DAP	1.03803	0.945
57DAP/52DAP	1.09504	0.601
57DAP/7DAP	1.14671	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80772	0.056
17DAP/reference	0.78827	0.011
27DAP/reference	0.731	0.01
39DAP/reference	0.91649	0.23
41DAP/reference	0.7609	0.038
42DAP/reference	0.73407	0.011
43DAP/reference	0.94737	0.305
47DAP/reference	1.41906	0.2
52DAP/reference	0.51339	0.012
57DAP/reference	0.58823	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.791	0.043
17DAP/reference	0.90278	0.26
27DAP/reference	1.16692	0.639
39DAP/reference	1.3426	0.044
41DAP/reference	1.28003	0.099
42DAP/reference	1.37875	0.022
43DAP/reference	0.70828	0.033
47DAP/reference	1.19874	0.029
52DAP/reference	1.11067	0.393
57DAP/reference	0.99515	0.789

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74503	0.027
17DAP/reference	0.8363	0.231
27DAP/reference	0.70657	0.031
39DAP/reference	1.02391	0.912
41DAP/reference	0.96883	0.512
42DAP/reference	1.18995	0.209
43DAP/reference	1.57326	0.011
47DAP/reference	2.01329	0.007
52DAP/reference	2.33251	0.029
57DAP/reference	1.79609	0.056

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.23332	0.966
26DAP/20DAP	1.19063	0.574
34DAP/26DAP	0.96331	0.936
51DAP/34DAP	0.98453	0.873
52DAP/51DAP	1.24618	0.142
53DAP/52DAP	0.97078	0.848
55DAP/53DAP	1.0941	0.656
57DAP/55DAP	1.0275	0.899
62DAP/57DAP	1.02621	0.935
68DAP/62DAP	1.26352	0.792
68DAP/14DAP	0.58141	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.73803	0.048

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.30765
Mature Green Tomato/Ripe Tomato	0.90312	0.446
Immature Eggplant/Mature Eggplant	17.8183	0.105
Ripe Pepper/Ripe Tomato	0.19888	0.224
Mature Eggplant/Ripe Tomato	0.06222

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	1.08477
4-1-1/M82	N/A	N/A
4-1/M82	1.16064
4-3-2/M82	0.69202
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.89113

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.06701	0.493
IL2-6/WTpooled	1.16393	0.531
IL7-5/WTpooled	1.19437	1
IL7-3/WTpooled	1.02229	1
IL12-4/WTpooled	1.14109	0.538
IL1-4/WTpooled	1.01298	1
WT/WTpooled	0.93031	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	0.80208	0.226

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	1.02274	1
DC3000/delta hrp 12h	0.8807	1
DC3000/delta hrp 24h	1.45515

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.40591	0.025
DC3000 delta B/DC3000 delta AB	0.55337	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.49423	0.693
Exp 60h	1.02214	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03993	1
Var 0h	1.29196	0.782
Var 12h I row2-row1	0.83614	0.418
Var 12h NI row2-row1	0.88409	0.546
Var 36h I row2-row1	1.0314	1
Var 36h NI row2-row1	1.39626	0.482
Var 60h I row2-row1	1.10452	0.562
Var 60h NI row2-row1	1.16504	0.904
Time course 0hI-0hNI	1.04134	0.852
Time course 12hI-12hNI	0.98032	0.886
Time course 36hI-36hNI	0.84927	0.093
Time course 60hI-60hNI	0.18398	0.005

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)	1.25537	0.372
transgenic ySAMdc/azygous control (breaker)	1.15104	1
transgenic ySAMdc/azygous control (red)	0.93294	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.31246	0.046

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.54459	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.39443	0.096
Manapal/WT (break)	1.37908	0.13
Manapal/WT (red)	1.39208	0.222