Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.11.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02059	0.901
27DAP/17DAP	0.95183	0.839
39DAP/27DAP	1.11089	0.965
41DAP/39DAP	1.01562	0.909
42DAP/41DAP	1.26017	0.868
43DAP/42DAP	0.93973	0.877
47DAP/43DAP	1.36332	0.576
52DAP/47DAP	0.77867	0.489
57DAP/52DAP	0.84636	0.591

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89026	0.254
17DAP/reference	0.77851	0.104
27DAP/reference	0.94123	0.484
39DAP/reference	0.86456	0.267
41DAP/reference	0.69356	0.065
42DAP/reference	0.89882	0.067
43DAP/reference	1.01347	0.942
47DAP/reference	1.06756	0.275
52DAP/reference	1.03438	0.633
57DAP/reference	1.15776	0.097

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.60854	0.036
27DAP/17DAP	0.84166	0.151
39DAP/27DAP	0.83438	0.094
41DAP/39DAP	1.04227	1
42DAP/41DAP	0.97495	0.753
43DAP/42DAP	0.96202	0.641
47DAP/43DAP	0.89881	0.447
52DAP/47DAP	0.97366	0.9
57DAP/52DAP	0.92999	0.321
57DAP/7DAP	0.73428	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95486	0.402
17DAP/reference	1.06205	1
27DAP/reference	1.03417	0.664
39DAP/reference	1.04073	0.779
41DAP/reference	1.06954	0.836
42DAP/reference	1.19304	0.233
43DAP/reference	1.09051	0.672
47DAP/reference	1.09904	0.745
52DAP/reference	0.99931	0.621
57DAP/reference	1.11285	0.04

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05938	0.67
17DAP/reference	1.04547	0.859
27DAP/reference	0.99623	0.686
39DAP/reference	0.88996	0.049
41DAP/reference	0.86059	0.156
42DAP/reference	0.95919	0.392
43DAP/reference	1.39308	0.103
47DAP/reference	1.00357	0.812
52DAP/reference	0.86776	0.086
57DAP/reference	1.06831	0.786

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04317	0.939
17DAP/reference	1.12511	0.215
27DAP/reference	1.4054	0.043
39DAP/reference	1.24938	0.022
41DAP/reference	1.06739	0.674
42DAP/reference	1.00839	1
43DAP/reference	1.05424	1
47DAP/reference	1.00605	0.667
52DAP/reference	0.9247	0.444
57DAP/reference	1.10467	0.581

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.18974	0.586
26DAP/20DAP	1.24724	1
34DAP/26DAP	1.44642	0.304
51DAP/34DAP	1.55784
52DAP/51DAP	1.02935	1
53DAP/52DAP	1.13783	0.91
55DAP/53DAP	0.68406	0.325
57DAP/55DAP	1.04934	0.955
62DAP/57DAP	1.14808	0.935
68DAP/62DAP	0.77458	0.211
68DAP/14DAP	0.569	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.54011	0.049

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.59115
Mature Green Tomato/Ripe Tomato	0.71784	0.132
Immature Eggplant/Mature Eggplant	0.74549	0.081
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.63748	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.12397	0.742
1-1-2/M82	1.08664	1
12-2/M82	0.89567	0.535
12-4/M82	0.94568	0.619
1-3/M82	0.93413	1
2-1-1/M82	0.65432	0.465
2-1/M82	0.93635	0.345
2-6/M82	0.88841	1
3-2/M82	0.87325
4-1-1/M82	0.90715	1
4-1/M82	1.10775	1
4-3-2/M82	0.85063	0.698
4-3/M82	0.87495	0.578
5-3/M82	0.95981	1
6-2/M82	0.49756
6-3/M82	0.98912	1
7-1/M82	0.99929
7-2/M82	0.77229
9-3-2/M82	0.9032	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.9342
IL2-6/WTpooled	0.71258	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.97901	1
IL12-4/WTpooled	0.81118	0.478
IL1-4/WTpooled	0.99821	1
WT/WTpooled	0.92065	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	0.84585	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06049	0.921
DC3000/delta hrp 6h	0.87869	0.95
DC3000/delta hrp 12h	0.96966	1
DC3000/delta hrp 24h	1.09445	0.383

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.0901	0.556
DC3000 delta B/DC3000 delta AB	1.12023	0.353

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01173	1
Exp 36h	N/A	N/A
Exp 60h	1.0927	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01283	1
Var 0h	0.6147	0.332
Var 12h I row2-row1	0.93633	0.353
Var 12h NI row2-row1	0.99585	1
Var 36h I row2-row1	1.17635	1
Var 36h NI row2-row1	1.08216	1
Var 60h I row2-row1	1.06201	1
Var 60h NI row2-row1	0.96275	1
Time course 0hI-0hNI	1.03567	0.799
Time course 12hI-12hNI	0.92522	0.387
Time course 36hI-36hNI	0.86971	0.025
Time course 60hI-60hNI	0.43283	0.005

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)	0.9858	0.862
transgenic ySAMdc/azygous control (breaker)	0.97973	1
transgenic ySAMdc/azygous control (red)	0.95693	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97847	0.313

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.91371	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.94004	1
Manapal/WT (break)	0.90891	1
Manapal/WT (red)	0.983	0.863