Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.13.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.28439	0.014
27DAP/17DAP	1.11372	0.872
39DAP/27DAP	1.14798	0.745
41DAP/39DAP	1.22907	0.468
42DAP/41DAP	1.06558	0.994
43DAP/42DAP	0.89978	0.801
47DAP/43DAP	1.16775	0.444
52DAP/47DAP	1.37092	0.559
57DAP/52DAP	1.08818	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.48608	0.027
17DAP/reference	0.56833	0.007
27DAP/reference	0.75774	0.018
39DAP/reference	0.86897	0.2
41DAP/reference	0.76188	0.065
42DAP/reference	0.7657	0.001
43DAP/reference	0.84439	0.058
47DAP/reference	0.75203	0.001
52DAP/reference	0.73632	0.016
57DAP/reference	0.91698	0.156

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89926	0.47
27DAP/17DAP	0.99171	0.943
39DAP/27DAP	1.28407	0.2
41DAP/39DAP	0.87945	0.412
42DAP/41DAP	0.80853	0.109
43DAP/42DAP	0.85035	0.399
47DAP/43DAP	0.98732	0.947
52DAP/47DAP	1.10999	0.81
57DAP/52DAP	1.04251	0.851
57DAP/7DAP	0.95626	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.6563	0.059
17DAP/reference	0.79752	0.072
27DAP/reference	1.03776	0.974
39DAP/reference	0.64316	0.011
41DAP/reference	0.62573	0.011
42DAP/reference	0.78844	0.015
43DAP/reference	0.5911	0.011
47DAP/reference	0.55463	0.033
52DAP/reference	0.46509	0.011
57DAP/reference	0.46189	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.5497	0.005
17DAP/reference	0.50235	0.003
27DAP/reference	0.6581	0.037
39DAP/reference	0.47437	0.009
41DAP/reference	0.66121	0.036
42DAP/reference	0.66044	0.03
43DAP/reference	1.19479	0.801
47DAP/reference	0.89145	0.083
52DAP/reference	0.58947	0.003
57DAP/reference	0.57369	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75847	0.034
17DAP/reference	0.70768	0.103
27DAP/reference	0.85812	0.049
39DAP/reference	0.7964	0.031
41DAP/reference	0.82263	0.058
42DAP/reference	0.9204	0.361
43DAP/reference	0.62557	0.021
47DAP/reference	0.53095	0.004
52DAP/reference	0.81357	0.268
57DAP/reference	0.56718	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10193	0.966
26DAP/20DAP	1.18928	0.493
34DAP/26DAP	0.90027	0.702
51DAP/34DAP	0.82455	0.197
52DAP/51DAP	0.76003	1
53DAP/52DAP	1.27493	0.179
55DAP/53DAP	1.10784	0.964
57DAP/55DAP	1.21088	0.682
62DAP/57DAP	0.97523	0.994
68DAP/62DAP	0.72986	0.227
68DAP/14DAP	0.63437	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.92317	0.358

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
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	0.93405	0.961
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.11327	1
1-3/M82	0.59047
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.87655
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	0.95465
5-3/M82	0.92083	1
6-2/M82	0.59698
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.83466
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	0.9836	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.99253	1
IL12-4/WTpooled	1.04314	0.646
IL1-4/WTpooled	0.9335	1
WT/WTpooled	0.99475	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	0.77506	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.14649	0.774
DC3000/delta hrp 6h	1.52279	0.582
DC3000/delta hrp 12h	0.71875	1
DC3000/delta hrp 24h	9.96905	0.024

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.3507	0.076
DC3000 delta B/DC3000 delta AB	1.14773	0.341

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.01488	1
Exp 60h	1.05485	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01524	1
Var 0h	0.89081	0.457
Var 12h I row2-row1	1.57137	0.189
Var 12h NI row2-row1	0.43258	0.36
Var 36h I row2-row1	1.00802	1
Var 36h NI row2-row1	2.67113	0.482
Var 60h I row2-row1	1.02427	1
Var 60h NI row2-row1	1.36142	0.281
Time course 0hI-0hNI	0.85757	0.334
Time course 12hI-12hNI	0.71378	0.173
Time course 36hI-36hNI	0.86001	0.119
Time course 60hI-60hNI	0.14582	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)	2.95951	1
transgenic ySAMdc/azygous control (breaker)	1.56145	1
transgenic ySAMdc/azygous control (red)	1.56227	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01302	0.723

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.64083	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.26762	0.307
Manapal/WT (break)	0.972	1
Manapal/WT (red)	N/A	N/A