Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.12.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05788	0.927
27DAP/17DAP	1.01616	1
39DAP/27DAP	0.81521	0.397
41DAP/39DAP	1.70621	0.236
42DAP/41DAP	1.29223	0.871
43DAP/42DAP	0.94212	0.834
47DAP/43DAP	0.91367	0.609
52DAP/47DAP	1.81346	0.147
57DAP/52DAP	0.90183	0.833

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.156	0.334
17DAP/reference	1.08332	0.185
27DAP/reference	0.97849	0.595
39DAP/reference	1.03547	0.628
41DAP/reference	1.2871	0.013
42DAP/reference	1.16816	0.041
43DAP/reference	1.0431	0.217
47DAP/reference	1.14688	0.114
52DAP/reference	1.02877	0.8
57DAP/reference	0.96067	0.415

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13585	0.205
27DAP/17DAP	0.84916	0.131
39DAP/27DAP	0.95889	0.775
41DAP/39DAP	0.96374	0.923
42DAP/41DAP	1.29441	0.06
43DAP/42DAP	0.81204	0.051
47DAP/43DAP	0.81019	0.156
52DAP/47DAP	2.00946	0.048
57DAP/52DAP	2.25209	0.038
57DAP/7DAP	1.61311	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89297	0.157
17DAP/reference	0.83207	0.035
27DAP/reference	0.85891	0.033
39DAP/reference	0.87188	0.083
41DAP/reference	0.92895	0.311
42DAP/reference	0.98004	0.506
43DAP/reference	0.8695	0.11
47DAP/reference	0.79754	0.079
52DAP/reference	0.76396	0.012
57DAP/reference	0.65999	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2599	0.113
17DAP/reference	1.51441	0.011
27DAP/reference	1.44083	0.032
39DAP/reference	1.4132	0.013
41DAP/reference	1.20968	0.234
42DAP/reference	1.27688	0.061
43DAP/reference	1.81907	0.128
47DAP/reference	1.32642	0.009
52DAP/reference	1.31682	0.043
57DAP/reference	1.80025	0.009

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94226	0.391
17DAP/reference	1.01026	0.778
27DAP/reference	0.75991	0.033
39DAP/reference	0.93928	0.36
41DAP/reference	0.90035	0.264
42DAP/reference	1.1975	0.089
43DAP/reference	1.20492	0.164
47DAP/reference	1.30084	0.028
52DAP/reference	0.98987	0.838
57DAP/reference	1.25155	0.255

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99316	1
26DAP/20DAP	2.27902	0.615
34DAP/26DAP	3.49811	1
51DAP/34DAP	1.03238	0.688
52DAP/51DAP	5.15317	0.033
53DAP/52DAP	0.62926	0.051
55DAP/53DAP	1.60871	0.039
57DAP/55DAP	0.5038	0.045
62DAP/57DAP	1.60806	0.158
68DAP/62DAP	2.01942	0.323
68DAP/14DAP	0.7472	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.1679	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.77089	0.23
Mature Green Tomato/Ripe Tomato	1.23657	0.752
Immature Eggplant/Mature Eggplant	1.61704	0.05
Ripe Pepper/Ripe Tomato	0.71946	0.293
Mature Eggplant/Ripe Tomato	1.64382	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.89441	0.616
1-1-2/M82	0.9212	1
12-2/M82	0.8091
12-4/M82	1.00058	1
1-3/M82	0.84536	0.441
2-1-1/M82	0.93023	0.683
2-1/M82	N/A	N/A
2-6/M82	1.32072	0.594
3-2/M82	0.88343
4-1-1/M82	1.15189	1
4-1/M82	0.84762	1
4-3-2/M82	0.84433	1
4-3/M82	0.77736	0.72
5-3/M82	0.89945	0.642
6-2/M82	0.91924	1
6-3/M82	1.01646	1
7-1/M82	0.9059
7-2/M82	0.97148	1
9-3-2/M82	0.70355	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.02632	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.93616	0.298
IL12-4/WTpooled	0.8833	0.581
IL1-4/WTpooled	1.01337	1
WT/WTpooled	1.02781	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	1.15308	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04066	1
DC3000/delta hrp 6h	1.14283	0.857
DC3000/delta hrp 12h	0.96933	1
DC3000/delta hrp 24h	1.00545	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.53306	0.076
DC3000 delta B/DC3000 delta AB	1.71115	0.081

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.87249	1
Exp 36h	0.91268	0.539
Exp 60h	0.80982	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99714	1
Var 0h	0.97497	1
Var 12h I row2-row1	0.74877	0.514
Var 12h NI row2-row1	0.94645	0.82
Var 36h I row2-row1	1.05552	1
Var 36h NI row2-row1	1.54736	0.276
Var 60h I row2-row1	1.09621	1
Var 60h NI row2-row1	0.96671	1
Time course 0hI-0hNI	0.85256	0.241
Time course 12hI-12hNI	1.04764	1
Time course 36hI-36hNI	0.8745	0.225
Time course 60hI-60hNI	0.58872	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)	0.83264	0.286
transgenic ySAMdc/azygous control (breaker)	0.91242	0.49
transgenic ySAMdc/azygous control (red)	0.97788	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98014	0.277

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.30186	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.68147	1
Manapal/WT (break)	0.81633	0.333
Manapal/WT (red)	0.88311	0.607