Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.8.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87958	0.551
27DAP/17DAP	1.18595	0.859
39DAP/27DAP	0.9206	0.487
41DAP/39DAP	1.61662	0.289
42DAP/41DAP	2.18245	0.056
43DAP/42DAP	1.99275	0.03
47DAP/43DAP	0.75565	0.298
52DAP/47DAP	0.57155	0.093
57DAP/52DAP	0.75816	0.613

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80798	0.098
17DAP/reference	1.28001	0.355
27DAP/reference	1.1516	0.487
39DAP/reference	1.26101	0.218
41DAP/reference	1.07936	0.516
42DAP/reference	1.29916	0.706
43DAP/reference	1.00594	0.942
47DAP/reference	0.98608	0.535
52DAP/reference	1.04245	0.766
57DAP/reference	0.8583	0.035

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0145	1
27DAP/17DAP	0.81815	0.39
39DAP/27DAP	1.04603	0.659
41DAP/39DAP	0.91833	0.764
42DAP/41DAP	1.36875	0.208
43DAP/42DAP	1.32681	0.038
47DAP/43DAP	1.0007	0.989
52DAP/47DAP	0.97362	0.905
57DAP/52DAP	1.05532	0.732
57DAP/7DAP	1.76516	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82502	0.122
17DAP/reference	1.09408	0.896
27DAP/reference	0.90166	0.135
39DAP/reference	0.88134	0.198
41DAP/reference	0.73844	0.023
42DAP/reference	0.80212	0.063
43DAP/reference	0.88183	0.21
47DAP/reference	0.87777	0.293
52DAP/reference	0.87129	0.097
57DAP/reference	0.91176	0.25

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9609	0.623
17DAP/reference	1.05088	0.508
27DAP/reference	0.94016	0.381
39DAP/reference	0.90997	0.129
41DAP/reference	0.9877	0.545
42DAP/reference	0.98414	0.534
43DAP/reference	1.03969	0.986
47DAP/reference	0.97032	0.423
52DAP/reference	1.00279	0.761
57DAP/reference	1.09341	0.626

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93787	0.311
17DAP/reference	0.95323	0.55
27DAP/reference	1.14871	0.408
39DAP/reference	0.81501	0.063
41DAP/reference	0.82729	0.033
42DAP/reference	0.89996	0.361
43DAP/reference	0.89801	0.237
47DAP/reference	0.89332	0.097
52DAP/reference	1.00133	0.732
57DAP/reference	0.70571	0.045

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.27688	0.24
26DAP/20DAP	1.13149	0.813
34DAP/26DAP	1.21275	1
51DAP/34DAP	1.37628	0.303
52DAP/51DAP	0.76498	1
53DAP/52DAP	0.93885	0.807
55DAP/53DAP	0.85317	0.35
57DAP/55DAP	0.91164	0.684
62DAP/57DAP	0.86403	0.162
68DAP/62DAP	1.03961	1
68DAP/14DAP	1.25851	0.802

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.0411	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.02932	1
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.1233	1
Mature Eggplant/Ripe Tomato	0.69113

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.54609
1-1-2/M82	1.01766	1
12-2/M82	N/A	N/A
12-4/M82	0.78111	0.358
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.73558
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.83483
5-3/M82	0.92612	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.86796
7-2/M82	0.89334
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.47838	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.96152	1
IL12-4/WTpooled	0.67892	0.554
IL1-4/WTpooled	0.22431	0.444
WT/WTpooled	0.94406	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	0.8917	0.256

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.24405	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.98771	1
DC3000/delta hrp 24h	1.10859	0.673

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.9676	1
Exp 60h	0.89423	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03326	1
Var 0h	0.91754	1
Var 12h I row2-row1	1.13991	0.58
Var 12h NI row2-row1	1.01571	1
Var 36h I row2-row1	1.15556	1
Var 36h NI row2-row1	0.63071	0.478
Var 60h I row2-row1	1.09001	0.287
Var 60h NI row2-row1	0.88008	0.866
Time course 0hI-0hNI	0.86919	0.266
Time course 12hI-12hNI	0.84696	0.113
Time course 36hI-36hNI	0.76951	0.047
Time course 60hI-60hNI	0.43998	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)	1.05191	0.699
transgenic ySAMdc/azygous control (breaker)	0.96072	1
transgenic ySAMdc/azygous control (red)	1.08125	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93804	0.112

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.12472	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.97167	1
Manapal/WT (break)	2.00374	0.14
Manapal/WT (red)	1.33399	0.15