Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.15.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98504	0.83
27DAP/17DAP	1.25468	0.749
39DAP/27DAP	1.2041	0.61
41DAP/39DAP	1.24996	0.498
42DAP/41DAP	1.06115	0.994
43DAP/42DAP	0.95434	0.877
47DAP/43DAP	0.934	0.687
52DAP/47DAP	1.2649	0.608
57DAP/52DAP	0.88282	0.85

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0148	0.787
17DAP/reference	1.07901	0.193
27DAP/reference	0.99334	0.797
39DAP/reference	1.04557	0.352
41DAP/reference	1.10667	0.287
42DAP/reference	0.88457	0.067
43DAP/reference	1.03966	0.705
47DAP/reference	0.85126	0.032
52DAP/reference	0.7955	0.089
57DAP/reference	0.75242	0.035

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91788	0.454
27DAP/17DAP	1.22556	0.37
39DAP/27DAP	1.09817	0.519
41DAP/39DAP	0.83695	0.246
42DAP/41DAP	0.98602	0.797
43DAP/42DAP	0.99072	0.96
47DAP/43DAP	0.99283	0.961
52DAP/47DAP	1.00165	0.947
57DAP/52DAP	0.94734	0.673
57DAP/7DAP	1.12358	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80882	0.066
17DAP/reference	0.77164	0.024
27DAP/reference	0.82502	0.018
39DAP/reference	0.73193	0.011
41DAP/reference	0.74661	0.026
42DAP/reference	0.64874	0.011
43DAP/reference	0.77079	0.02
47DAP/reference	0.92822	0.383
52DAP/reference	0.71739	0.021
57DAP/reference	0.66552	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1392	0.23
17DAP/reference	1.10956	0.338
27DAP/reference	0.89984	0.229
39DAP/reference	0.81769	0.136
41DAP/reference	0.78271	0.047
42DAP/reference	0.84211	0.032
43DAP/reference	1.25223	0.093
47DAP/reference	1.00725	1
52DAP/reference	0.93747	0.121
57DAP/reference	1.4719	0.101

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83694	0.045
17DAP/reference	0.96709	0.579
27DAP/reference	0.81406	0.045
39DAP/reference	0.80182	0.011
41DAP/reference	0.83926	0.028
42DAP/reference	0.72629	0.036
43DAP/reference	0.69425	0.025
47DAP/reference	1.04776	0.82
52DAP/reference	0.78889	0.132
57DAP/reference	0.49601	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06682	0.966
26DAP/20DAP	1.06543	1
34DAP/26DAP	0.94333	0.898
51DAP/34DAP	1.12547	0.677
52DAP/51DAP	1.03282	0.848
53DAP/52DAP	1.03498	0.868
55DAP/53DAP	1.0927	0.79
57DAP/55DAP	0.94338	0.736
62DAP/57DAP	0.98047	0.994
68DAP/62DAP	0.87158	0.543
68DAP/14DAP	0.64103	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.82632	0.155

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.81431	0.265
Mature Green Tomato/Ripe Tomato	1.34343	0.028
Immature Eggplant/Mature Eggplant	1.65435	0.05
Ripe Pepper/Ripe Tomato	9.97088	0.235
Mature Eggplant/Ripe Tomato	1.32439

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.88675	0.944
1-1-2/M82	0.95448
12-2/M82	1.33018	0.405
12-4/M82	1.09524	1
1-3/M82	0.86361	0.501
2-1-1/M82	1.28623	0.689
2-1/M82	N/A	N/A
2-6/M82	1.10626	0.695
3-2/M82	N/A	N/A
4-1-1/M82	1.09199	1
4-1/M82	1.19585
4-3-2/M82	1.01196	1
4-3/M82	1.11176
5-3/M82	0.9269	1
6-2/M82	0.73257	0.481
6-3/M82	1.01202	1
7-1/M82	N/A	N/A
7-2/M82	0.9696	1
9-3-2/M82	0.95976	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.20553	0.427
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.81894	0.418
IL12-4/WTpooled	1.15205	0.538
IL1-4/WTpooled	1.16887	1
WT/WTpooled	1.04563	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	1.0216	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07802	0.823
DC3000/delta hrp 6h	1.18571	0.95
DC3000/delta hrp 12h	1.16495	1
DC3000/delta hrp 24h	1.02238	0.743

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.18098	0.355
DC3000 delta B/DC3000 delta AB	1.19447	0.292

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00154	1
Exp 36h	0.97065	0.82
Exp 60h	1.08582	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01196	1
Var 0h	2.49799	0.936
Var 12h I row2-row1	1.07593	0.215
Var 12h NI row2-row1	0.88011	0.394
Var 36h I row2-row1	1.12767	0.908
Var 36h NI row2-row1	1.16635	1
Var 60h I row2-row1	1.15217	0.543
Var 60h NI row2-row1	1.11332	0.904
Time course 0hI-0hNI	1.08322	0.603
Time course 12hI-12hNI	0.91835	0.387
Time course 36hI-36hNI	0.9126	0.265
Time course 60hI-60hNI	0.98101	0.646

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)	0.92541	0.377
transgenic ySAMdc/azygous control (breaker)	0.87763	0.251
transgenic ySAMdc/azygous control (red)	0.92324	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03011	0.185

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.90865	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	0.74878	1
Manapal/WT (red)	0.67132	0.181