Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.8.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94842	0.689
27DAP/17DAP	1.28095	0.742
39DAP/27DAP	0.80935	0.449
41DAP/39DAP	1.26394	0.413
42DAP/41DAP	1.2435	0.871
43DAP/42DAP	0.89657	0.788
47DAP/43DAP	0.82268	0.467
52DAP/47DAP	1.85883	0.156
57DAP/52DAP	0.88107	0.845

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9144	0.177
17DAP/reference	0.956	0.278
27DAP/reference	0.88788	0.083
39DAP/reference	0.91868	0.412
41DAP/reference	0.95224	0.434
42DAP/reference	0.91472	0.012
43DAP/reference	1.01953	0.928
47DAP/reference	0.88273	0.011
52DAP/reference	0.8082	0.019
57DAP/reference	0.81635	0.024

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98181	0.763
27DAP/17DAP	0.95906	0.878
39DAP/27DAP	1.0105	0.862
41DAP/39DAP	0.99226	1
42DAP/41DAP	1.03609	1
43DAP/42DAP	1.21724	0.212
47DAP/43DAP	1.05518	0.822
52DAP/47DAP	0.87612	0.446
57DAP/52DAP	0.9139	0.494
57DAP/7DAP	0.82168	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89638	0.168
17DAP/reference	0.90251	0.22
27DAP/reference	0.77966	0.048
39DAP/reference	0.86561	0.064
41DAP/reference	0.84432	0.043
42DAP/reference	0.76346	0.029
43DAP/reference	0.80444	0.018
47DAP/reference	0.67454	0.079
52DAP/reference	0.67934	0.012
57DAP/reference	0.78517	0.016

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10056	0.249
17DAP/reference	0.93708	0.063
27DAP/reference	0.89266	0.129
39DAP/reference	0.87769	0.132
41DAP/reference	0.92031	0.169
42DAP/reference	0.89447	0.108
43DAP/reference	0.981	0.657
47DAP/reference	0.99518	0.678
52DAP/reference	0.90271	0.143
57DAP/reference	1.167	0.286

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80574	0.057
17DAP/reference	1.01961	0.886
27DAP/reference	0.86445	0.065
39DAP/reference	0.773	0.028
41DAP/reference	0.8819	0.209
42DAP/reference	0.77166	0.071
43DAP/reference	0.6185	0.019
47DAP/reference	0.92747	0.357
52DAP/reference	0.7851	0.139
57DAP/reference	0.64203	0.025

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91127	0.44
26DAP/20DAP	1.10143	0.735
34DAP/26DAP	1.18412	0.819
51DAP/34DAP	1.27046	0.185
52DAP/51DAP	0.98074	1
53DAP/52DAP	1.25028	0.58
55DAP/53DAP	1.04806	0.876
57DAP/55DAP	0.98654	0.914
62DAP/57DAP	1.0703	0.622
68DAP/62DAP	1.17574	0.523
68DAP/14DAP	1.24742	0.578

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.78839	0.097

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.99345	0.765
Mature Green Tomato/Ripe Tomato	0.89211	0.411
Immature Eggplant/Mature Eggplant	1.72269	0.053
Ripe Pepper/Ripe Tomato	1.14245	1
Mature Eggplant/Ripe Tomato	1.17228	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96013
1-1-2/M82	1.05498	0.977
12-2/M82	1.07413	1
12-4/M82	1.02821	1
1-3/M82	0.81286	0.378
2-1-1/M82	1.35545
2-1/M82	N/A	N/A
2-6/M82	1.09543	0.505
3-2/M82	N/A	N/A
4-1-1/M82	1.04799	1
4-1/M82	0.92906	1
4-3-2/M82	0.91362	1
4-3/M82	0.87369	1
5-3/M82	1.08762	1
6-2/M82	0.9918
6-3/M82	0.98574	1
7-1/M82	1.21072
7-2/M82	0.97064	1
9-3-2/M82	0.89472	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.82207	1
IL2-6/WTpooled	0.95036	1
IL7-5/WTpooled	1.24676	0.792
IL7-3/WTpooled	0.7103	0.31
IL12-4/WTpooled	0.93818	0.71
IL1-4/WTpooled	0.93563	0.834
WT/WTpooled	0.9364	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	1.25772	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00499	1
DC3000/delta hrp 6h	1.38043	1
DC3000/delta hrp 12h	1.04372	1
DC3000/delta hrp 24h	1.10944	0.296

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.99038	0.955
DC3000 delta B/DC3000 delta AB	0.9244	0.369

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.09946	1
Exp 36h	0.97878	0.943
Exp 60h	0.92021	0.32

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98385	1
Var 0h	0.9201	1
Var 12h I row2-row1	1.00907	1
Var 12h NI row2-row1	0.95909	0.713
Var 36h I row2-row1	0.94346	1
Var 36h NI row2-row1	1.19172	1
Var 60h I row2-row1	1.16934	0.562
Var 60h NI row2-row1	0.99264	1
Time course 0hI-0hNI	0.96661	0.754
Time course 12hI-12hNI	0.95663	0.431
Time course 36hI-36hNI	0.85765	0.099
Time course 60hI-60hNI	0.7126	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)	0.93292	0.306
transgenic ySAMdc/azygous control (breaker)	0.96898	1
transgenic ySAMdc/azygous control (red)	1.02535	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0156	0.372

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.09905	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.96806	1
Manapal/WT (break)	1.0641	1
Manapal/WT (red)	0.98123	0.863