Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.15.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.71311	0.078
27DAP/17DAP	1.04158	1
39DAP/27DAP	1.39983	0.789
41DAP/39DAP	1.25102	0.642
42DAP/41DAP	0.86503	1
43DAP/42DAP	0.94765	0.877
47DAP/43DAP	1.10197	0.965
52DAP/47DAP	1.3675	0.615
57DAP/52DAP	0.83406	0.759

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10524	0.334
17DAP/reference	1.12409	0.138
27DAP/reference	1.10746	0.426
39DAP/reference	1.09511	0.262
41DAP/reference	1.26108	0.023
42DAP/reference	1.21022	0.001
43DAP/reference	1.05417	0.705
47DAP/reference	1.05542	0.627
52DAP/reference	1.0095	1
57DAP/reference	1.05701	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02264	1
27DAP/17DAP	0.88096	0.39
39DAP/27DAP	0.95991	0.732
41DAP/39DAP	1.01565	0.909
42DAP/41DAP	1.05671	0.783
43DAP/42DAP	0.98374	0.854
47DAP/43DAP	1.02971	0.973
52DAP/47DAP	0.90726	0.482
57DAP/52DAP	0.83957	0.346
57DAP/7DAP	0.92329	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93957	0.326
17DAP/reference	0.96514	0.338
27DAP/reference	0.90712	0.055
39DAP/reference	0.88717	0.126
41DAP/reference	0.87237	0.013
42DAP/reference	0.88648	0.015
43DAP/reference	0.87148	0.1
47DAP/reference	1.01083	1
52DAP/reference	0.9656	0.363
57DAP/reference	0.7818	0.025

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12707	0.289
17DAP/reference	1.33567	0.176
27DAP/reference	1.34407	0.2
39DAP/reference	1.04082	1
41DAP/reference	1.13416	0.382
42DAP/reference	1.15591	0.274
43DAP/reference	1.36938	0.099
47DAP/reference	1.22435	0.024
52DAP/reference	1.08394	0.667
57DAP/reference	0.97746	0.61

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97386	0.489
17DAP/reference	1.12344	0.531
27DAP/reference	0.81919	0.048
39DAP/reference	0.82249	0.026
41DAP/reference	1.05704	0.754
42DAP/reference	1.15819	0.51
43DAP/reference	1.13328	0.524
47DAP/reference	0.97678	0.478
52DAP/reference	0.82819	0.22
57DAP/reference	1.07145	0.786

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07415	1
26DAP/20DAP	0.90868	1
34DAP/26DAP	1.01738	1
51DAP/34DAP	0.7833	0.449
52DAP/51DAP	1.27666	0.09
53DAP/52DAP	1.09312	0.819
55DAP/53DAP	1.13253	0.452
57DAP/55DAP	0.95815	0.694
62DAP/57DAP	0.8773	0.681
68DAP/62DAP	1.01253	1
68DAP/14DAP	0.46047

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.09281	0.7

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.87527	0.487
Immature Eggplant/Mature Eggplant	0.89373	0.079
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06377	0.877
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.12011
1-3/M82	0.75785
2-1-1/M82	0.64064
2-1/M82	N/A	N/A
2-6/M82	0.9359
3-2/M82	1.01854	0.967
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.15018
4-3/M82	N/A	N/A
5-3/M82	0.90794	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	N/A	N/A
9-3-2/M82	0.85525	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.254	0.277
IL2-6/WTpooled	0.92214	0.473
IL7-5/WTpooled	1.00135	1
IL7-3/WTpooled	1.10518	1
IL12-4/WTpooled	1.19083	0.557
IL1-4/WTpooled	1.14743	1
WT/WTpooled	0.96072	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	0.88134	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0981	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.94021	1
DC3000/delta hrp 24h	1.41561	0.036

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.51202	0.11
DC3000 delta B/DC3000 delta AB	1.12295	0.315

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.12358	1
Exp 36h	1.17191	1
Exp 60h	0.84335	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.82006	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.07241	0.748
transgenic ySAMdc/azygous control (breaker)	1.13718	1
transgenic ySAMdc/azygous control (red)	1.0919	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.89321	0.049

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.05664	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.61289	0.093
Manapal/WT (break)	1.27462	0.381
Manapal/WT (red)	N/A	N/A