Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.12.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81324	0.26
27DAP/17DAP	1.19165	0.833
39DAP/27DAP	1.72576	0.201
41DAP/39DAP	0.94401	0.65
42DAP/41DAP	1.02011	1
43DAP/42DAP	0.76867	0.589
47DAP/43DAP	0.50885	0.049
52DAP/47DAP	1.60697	0.335
57DAP/52DAP	0.81212	0.754

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12918	0.23
17DAP/reference	0.85955	0.065
27DAP/reference	0.96477	0.567
39DAP/reference	0.9538	0.37
41DAP/reference	0.8294	0.009
42DAP/reference	1.50436	0.001
43DAP/reference	0.84551	0.032
47DAP/reference	0.90734	0.098
52DAP/reference	1.00757	0.668
57DAP/reference	1.04714	0.249

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89282	0.158
27DAP/17DAP	1.01748	0.969
39DAP/27DAP	0.97552	0.812
41DAP/39DAP	1.0412	0.861
42DAP/41DAP	0.98403	0.791
43DAP/42DAP	0.87332	0.189
47DAP/43DAP	1.05578	0.906
52DAP/47DAP	1.56699	0.101
57DAP/52DAP	2.7443	0.029
57DAP/7DAP	1.84759	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88905	0.27
17DAP/reference	1.15897	0.328
27DAP/reference	1.01431	1
39DAP/reference	1.34045	0.012
41DAP/reference	1.10696	0.524
42DAP/reference	1.56883	0.013
43DAP/reference	1.995	0.006
47DAP/reference	1.07194	0.885
52DAP/reference	1.28575	0.043
57DAP/reference	1.89985	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99638	0.884
17DAP/reference	1.28043	0.156
27DAP/reference	1.24211	0.09
39DAP/reference	1.43876	0.011
41DAP/reference	1.44439	0.012
42DAP/reference	1.28187	0.118
43DAP/reference	1.31164	0.029
47DAP/reference	1.18594	0.205
52DAP/reference	0.88174	0.055
57DAP/reference	0.80323	0.073

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88925	0.059
17DAP/reference	0.95913	0.579
27DAP/reference	1.27626	0.028
39DAP/reference	1.19062	0.038
41DAP/reference	1.13334	0.521
42DAP/reference	1.17289	0.124
43DAP/reference	1.29291	0.291
47DAP/reference	0.95229	0.409
52DAP/reference	1.28801	0.071
57DAP/reference	1.64917	0.012

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01115	1
26DAP/20DAP	1.37012	0.153
34DAP/26DAP	0.89601	0.399
51DAP/34DAP	1.10981	0.898
52DAP/51DAP	1.1023	0.808
53DAP/52DAP	1.02018	1
55DAP/53DAP	0.89715	0.604
57DAP/55DAP	1.0352	0.975
62DAP/57DAP	1.24983	0.723
68DAP/62DAP	1.06475	0.939
68DAP/14DAP	2.09556	0.265

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.21161	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.59901	0.089
Mature Green Tomato/Ripe Tomato	1.22562	0.632
Immature Eggplant/Mature Eggplant	0.784	0.159
Ripe Pepper/Ripe Tomato	0.19699	0.224
Mature Eggplant/Ripe Tomato	0.24878	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.11512	0.877
1-1-2/M82	1.13126	1
12-2/M82	1.43045	1
12-4/M82	0.96956	1
1-3/M82	1.0753	1
2-1-1/M82	1.19256	0.764
2-1/M82	1.21748	1
2-6/M82	0.87787	0.501
3-2/M82	0.93964
4-1-1/M82	0.81618	1
4-1/M82	1.27622	0.853
4-3-2/M82	1.09094	1
4-3/M82	1.00717	1
5-3/M82	0.84285	0.447
6-2/M82	0.7977	0.473
6-3/M82	1.05546
7-1/M82	0.68405
7-2/M82	0.81383	0.599
9-3-2/M82	0.89162	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.11513	0.659
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.94137	1
IL12-4/WTpooled	0.64572	0.484
IL1-4/WTpooled	0.90523	0.435
WT/WTpooled	0.96692	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	0.92774	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09686	0.921
DC3000/delta hrp 6h	1.0035	0.95
DC3000/delta hrp 12h	0.82218	1
DC3000/delta hrp 24h	1.79509	0.03

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.30076	0.042
DC3000 delta B/DC3000 delta AB	1.13049	0.308

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.80795	0.328
Exp 36h	0.87741	0.661
Exp 60h	0.84372	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00917	1
Var 0h	0.76896	1
Var 12h I row2-row1	1.11469	0.692
Var 12h NI row2-row1	1.21316	0.649
Var 36h I row2-row1	0.73244	0.805
Var 36h NI row2-row1	0.55971	0.308
Var 60h I row2-row1	0.92571	0.439
Var 60h NI row2-row1	1.09245	1
Time course 0hI-0hNI	1.06737	0.603
Time course 12hI-12hNI	0.88583	0.239
Time course 36hI-36hNI	0.57496	0.023
Time course 60hI-60hNI	1.9021	0.008

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)	1.45801	0.3
transgenic ySAMdc/azygous control (breaker)	0.87189	0.251
transgenic ySAMdc/azygous control (red)	1.25522	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03863	0.448

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.99068	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.70892	1
Manapal/WT (break)	1.12385	1
Manapal/WT (red)	0.50571	0.181