Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.2.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.2407	0.67
27DAP/17DAP	1.24228	0.804
39DAP/27DAP	0.8596	0.573
41DAP/39DAP	0.88327	0.527
42DAP/41DAP	1.095	0.967
43DAP/42DAP	1.25179	0.58
47DAP/43DAP	1.61047	0.309
52DAP/47DAP	0.84509	0.587
57DAP/52DAP	1.2646	0.837

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14844	0.567
17DAP/reference	1.34074	0.565
27DAP/reference	0.99551	0.822
39DAP/reference	1.23415	0.445
41DAP/reference	1.04008	0.624
42DAP/reference	1.1505	0.585
43DAP/reference	1.18141	0.596
47DAP/reference	1.42514	0.096
52DAP/reference	1.30477	0.388
57DAP/reference	1.16325	0.3

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17351	0.068
27DAP/17DAP	0.94335	0.821
39DAP/27DAP	0.7604	0.032
41DAP/39DAP	1.23145	0.469
42DAP/41DAP	0.98769	0.83
43DAP/42DAP	1.04905	0.788
47DAP/43DAP	0.89679	0.225
52DAP/47DAP	1.03743	0.965
57DAP/52DAP	1.01241	1
57DAP/7DAP	1.01169

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.57902	0.025
17DAP/reference	1.33372	0.008
27DAP/reference	1.52943	0.009
39DAP/reference	1.44768	0.007
41DAP/reference	1.34128	0.038
42DAP/reference	1.74926	0.007
43DAP/reference	1.49804	0.029
47DAP/reference	1.27418	0.292
52DAP/reference	1.8835	0.007
57DAP/reference	1.4589	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.63019	0.634
17DAP/reference	1.0922	0.904
27DAP/reference	0.93544	0.423
39DAP/reference	1.23351	0.2
41DAP/reference	1.17241	0.416
42DAP/reference	0.68913	0.108
43DAP/reference	0.98044	0.62
47DAP/reference	1.05046	0.994
52DAP/reference	1.20461	0.24
57DAP/reference	1.1317	0.462

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.41999	0.079
17DAP/reference	1.02708	0.792
27DAP/reference	0.98221	0.727
39DAP/reference	1.1842	0.041
41DAP/reference	1.4246	0.05
42DAP/reference	1.38127	0.049
43DAP/reference	1.23354	0.121
47DAP/reference	1.2248	0.055
52DAP/reference	1.19465	0.318
57DAP/reference	1.57454	0.043

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.80349	1
26DAP/20DAP	1.00798	1
34DAP/26DAP	0.94338	0.861
51DAP/34DAP	0.99945	0.957
52DAP/51DAP	0.97066	1
53DAP/52DAP	1.0528	0.845
55DAP/53DAP	0.87191	0.592
57DAP/55DAP	1.45989	0.694
62DAP/57DAP	0.92624	0.681
68DAP/62DAP	0.90371	0.863
68DAP/14DAP	1.08598	0.739

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.25021	0.198

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.61481	0.086
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.59384
Mature Eggplant/Ripe Tomato	0.48459

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97367
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.88153	0.619
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	N/A	N/A
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	1.06003	1
5-3/M82	1.13827
6-2/M82	N/A	N/A
6-3/M82	0.97629
7-1/M82	1.15796
7-2/M82	0.99206
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.43162
IL2-6/WTpooled	0.98367	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.01651	1
IL12-4/WTpooled	1.0233	1
IL1-4/WTpooled	0.83822	0.699
WT/WTpooled	0.94462	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	0.85924	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05797	0.914
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.12649	1
DC3000/delta hrp 24h	1.01518	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.51883	0.025
DC3000 delta B/DC3000 delta AB	0.53931	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.68165	0.406
Exp 60h	0.91481	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99748	1
Var 0h	0.44533	0.232
Var 12h I row2-row1	0.85727	0.514
Var 12h NI row2-row1	1.02902	1
Var 36h I row2-row1	0.85998	0.805
Var 36h NI row2-row1	1.19086	0.482
Var 60h I row2-row1	0.94838	0.832
Var 60h NI row2-row1	1.17658	0.904
Time course 0hI-0hNI	0.97972	0.94
Time course 12hI-12hNI	1.03842	0.773
Time course 36hI-36hNI	0.91514	0.134
Time course 60hI-60hNI	0.24943	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)	0.92666	0.409
transgenic ySAMdc/azygous control (breaker)	1.08412	1
transgenic ySAMdc/azygous control (red)	1.1152	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93967	0.063

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.49136	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.31465	0.083
Manapal/WT (break)	2.43498	0.123
Manapal/WT (red)	1.14256	1