Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.3.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05241	0.927
27DAP/17DAP	1.20523	0.866
39DAP/27DAP	1.35889	0.663
41DAP/39DAP	1.75512	0.285
42DAP/41DAP	1.11771	0.967
43DAP/42DAP	0.86334	0.786
47DAP/43DAP	0.77998	0.33
52DAP/47DAP	1.78667	0.264
57DAP/52DAP	0.8043	0.778

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8088	0.025
17DAP/reference	0.89991	0.043
27DAP/reference	0.89595	0.129
39DAP/reference	0.85306	0.088
41DAP/reference	0.8387	0.009
42DAP/reference	1.07308	1
43DAP/reference	0.50968	0.148
47DAP/reference	1.17606	0.254
52DAP/reference	1.2853	0.059
57DAP/reference	1.83848

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95464	0.629
27DAP/17DAP	1.10816	0.885
39DAP/27DAP	0.9957	1
41DAP/39DAP	0.94765	0.849
42DAP/41DAP	0.96798	0.721
43DAP/42DAP	0.88333	0.116
47DAP/43DAP	1.01115	0.963
52DAP/47DAP	1.02496	0.965
57DAP/52DAP	0.86223	0.219
57DAP/7DAP	0.86028	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77639	0.08
17DAP/reference	0.72143	0.012
27DAP/reference	0.78555	0.012
39DAP/reference	0.74264	0.012
41DAP/reference	0.70231	0.021
42DAP/reference	0.59754	0.01
43DAP/reference	0.60266	0.013
47DAP/reference	0.87366	0.383
52DAP/reference	0.66984	0.017
57DAP/reference	0.61793	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04508	0.626
17DAP/reference	0.90551	0.059
27DAP/reference	1.2304	0.412
39DAP/reference	1.22276	0.136
41DAP/reference	1.16487	0.188
42DAP/reference	1.15126	0.226
43DAP/reference	1.03782	0.875
47DAP/reference	0.8804	0.028
52DAP/reference	1.03104	0.988
57DAP/reference	0.93417	0.361

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.73134	0.028
17DAP/reference	0.94283	0.364
27DAP/reference	0.71797	0.02
39DAP/reference	0.67789	0.008
41DAP/reference	0.81934	0.023
42DAP/reference	0.84131	0.108
43DAP/reference	0.93286	0.416
47DAP/reference	0.95808	0.357
52DAP/reference	0.71228	0.145
57DAP/reference	1.44737	0.09

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09008	0.966
26DAP/20DAP	0.89589	0.317
34DAP/26DAP	0.85368	0.112
51DAP/34DAP	0.89179	0.606
52DAP/51DAP	1.20142	0.503
53DAP/52DAP	0.96134	0.776
55DAP/53DAP	1.09964	0.622
57DAP/55DAP	0.98988	0.859
62DAP/57DAP	1.07559	0.833
68DAP/62DAP	1.46367	0.345
68DAP/14DAP	2.97125	0.024

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.6688	0.036

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.07594	0.287
Mature Green Tomato/Ripe Tomato	1.06119	0.948
Immature Eggplant/Mature Eggplant	1.16288	0.198
Ripe Pepper/Ripe Tomato	1.84224	0.258
Mature Eggplant/Ripe Tomato	1.52119	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.89226
1-1-2/M82	1.09688
12-2/M82	0.86146
12-4/M82	0.90042	1
1-3/M82	0.71356
2-1-1/M82	1.90504
2-1/M82	N/A	N/A
2-6/M82	0.91583	1
3-2/M82	N/A	N/A
4-1-1/M82	1.26197
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.03311	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.92807
9-3-2/M82	0.64778

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.25921	0.365
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.39307	0.75
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.49616
IL1-4/WTpooled	1.29544	0.426
WT/WTpooled	N/A	N/A

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	1.07569	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02045	0.921
DC3000/delta hrp 6h	1.09338	1
DC3000/delta hrp 12h	1.11068	1
DC3000/delta hrp 24h	1.04972	0.62

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.87097	0.882
DC3000 delta B/DC3000 delta AB	0.88436	0.326

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.09817	1
Exp 36h	1.02166	1
Exp 60h	1.17788	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98175	1
Var 0h	0.89615	1
Var 12h I row2-row1	0.99333	1
Var 12h NI row2-row1	0.97484	0.82
Var 36h I row2-row1	0.8518	0.805
Var 36h NI row2-row1	1.04718	1
Var 60h I row2-row1	1.10481	0.562
Var 60h NI row2-row1	1.00965	1
Time course 0hI-0hNI	0.98516	0.962
Time course 12hI-12hNI	0.90138	0.239
Time course 36hI-36hNI	0.88086	0.078
Time course 60hI-60hNI	0.70864	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)	0.98212	0.662
transgenic ySAMdc/azygous control (breaker)	0.8059	0.139
transgenic ySAMdc/azygous control (red)	0.89508	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03648	0.301

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.84053	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.9797	1
Manapal/WT (break)	0.95313	0.299
Manapal/WT (red)	1.06709	0.413