Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.14.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91502	0.503
27DAP/17DAP	0.8143	0.536
39DAP/27DAP	0.95049	0.652
41DAP/39DAP	1.44261	0.229
42DAP/41DAP	1.0659	1
43DAP/42DAP	0.8846	0.741
47DAP/43DAP	1.06603	0.926
52DAP/47DAP	1.61865	0.205
57DAP/52DAP	0.89741	0.778

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97259	0.513
17DAP/reference	1.06948	0.22
27DAP/reference	0.95371	0.257
39DAP/reference	1.09397	0.122
41DAP/reference	1.00636	1
42DAP/reference	0.96064	0.139
43DAP/reference	1.09811	0.05
47DAP/reference	1.09145	0.119
52DAP/reference	0.88402	0.135
57DAP/reference	0.82679	0.034

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92671	0.428
27DAP/17DAP	0.95471	0.821
39DAP/27DAP	1.07153	0.57
41DAP/39DAP	1.13461	0.799
42DAP/41DAP	1.20682	0.687
43DAP/42DAP	1.08598	0.413
47DAP/43DAP	1.10285	0.724
52DAP/47DAP	1.01912	1
57DAP/52DAP	1.03033	0.899
57DAP/7DAP	1.13002	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85719	0.077
17DAP/reference	0.91101	0.031
27DAP/reference	0.89553	0.017
39DAP/reference	0.89614	0.021
41DAP/reference	0.85277	0.018
42DAP/reference	0.83628	0.03
43DAP/reference	0.8177	0.017
47DAP/reference	0.86218	0.079
52DAP/reference	0.90002	0.049
57DAP/reference	0.88008	0.093

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10767	0.21
17DAP/reference	1.21295	0.139
27DAP/reference	0.93641	0.292
39DAP/reference	0.90013	0.235
41DAP/reference	0.80847	0.078
42DAP/reference	0.83147	0.017
43DAP/reference	1.32065	0.022
47DAP/reference	0.88692	0.023
52DAP/reference	1.05005	0.393
57DAP/reference	1.31994	0.094

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94788	0.335
17DAP/reference	1.0059	0.918
27DAP/reference	0.86516	0.039
39DAP/reference	0.86243	0.029
41DAP/reference	0.90316	0.086
42DAP/reference	0.87075	0.22
43DAP/reference	0.86346	0.165
47DAP/reference	0.88945	0.24
52DAP/reference	0.83788	0.158
57DAP/reference	0.57712	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16139	0.966
26DAP/20DAP	0.93307	0.512
34DAP/26DAP	1.02264	1
51DAP/34DAP	0.85663	0.085
52DAP/51DAP	1.07172	0.534
53DAP/52DAP	1.25449	0.24
55DAP/53DAP	1.05513	0.991
57DAP/55DAP	0.95018	0.789
62DAP/57DAP	1.27922	0.303
68DAP/62DAP	0.97521	0.863
68DAP/14DAP	1.13253	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.87696	0.175

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.44073	0.089
Mature Green Tomato/Ripe Tomato	0.70356	0.132
Immature Eggplant/Mature Eggplant	0.94951	0.808
Ripe Pepper/Ripe Tomato	0.74491	0.293
Mature Eggplant/Ripe Tomato	1.00854	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0627	0.877
1-1-2/M82	0.97082	1
12-2/M82	1.22944
12-4/M82	0.94602	1
1-3/M82	0.83881	0.378
2-1-1/M82	0.91348	0.465
2-1/M82	1.16093
2-6/M82	1.09504	0.594
3-2/M82	1.02418	1
4-1-1/M82	0.9095	1
4-1/M82	1.00091	1
4-3-2/M82	0.8202	0.698
4-3/M82	0.65466
5-3/M82	0.99714	1
6-2/M82	0.88461	1
6-3/M82	1.04553	1
7-1/M82	0.96643
7-2/M82	1.04302	1
9-3-2/M82	0.81697	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.02394	1
IL2-6/WTpooled	1.06317	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.865	0.31
IL12-4/WTpooled	1.15559	0.673
IL1-4/WTpooled	0.89134	0.834
WT/WTpooled	1.20531	0.713

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	0.96169	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92039	1
DC3000/delta hrp 6h	1.05012	1
DC3000/delta hrp 12h	1.12605	1
DC3000/delta hrp 24h	0.99548	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.03399	0.648
DC3000 delta B/DC3000 delta AB	0.87806	0.167

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0091	1
Exp 36h	0.67162	0.406
Exp 60h	1.07554	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98346	1
Var 0h	0.98719	1
Var 12h I row2-row1	1.1069	0.406
Var 12h NI row2-row1	0.95384	0.906
Var 36h I row2-row1	0.77105	0.805
Var 36h NI row2-row1	0.83048	0.584
Var 60h I row2-row1	1.24197	0.562
Var 60h NI row2-row1	1.09975	0.904
Time course 0hI-0hNI	1.03495	0.852
Time course 12hI-12hNI	1.04992	0.703
Time course 36hI-36hNI	0.91804	0.125
Time course 60hI-60hNI	1.03745	0.495

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)	1.18239	0.699
transgenic ySAMdc/azygous control (breaker)	1.09147	1
transgenic ySAMdc/azygous control (red)	1.04589	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98975	0.286

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.02351	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89503	1
Manapal/WT (break)	1.04295	1
Manapal/WT (red)	1.16209	0.222