Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.3.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01861	0.975
27DAP/17DAP	1.12073	0.849
39DAP/27DAP	1.01251	1
41DAP/39DAP	1.19627	0.85
42DAP/41DAP	1.1433	0.938
43DAP/42DAP	0.94265	0.874
47DAP/43DAP	1.12526	0.889
52DAP/47DAP	0.94086	0.837
57DAP/52DAP	0.84463	0.759

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9052	0.182
17DAP/reference	0.90868	0.24
27DAP/reference	1.01302	0.863
39DAP/reference	0.95991	0.467
41DAP/reference	0.86278	0.031
42DAP/reference	0.94905	0.091
43DAP/reference	0.93569	0.234
47DAP/reference	0.92134	0.05
52DAP/reference	1.09608	0.096
57DAP/reference	1.17305	0.097

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87067	0.509
27DAP/17DAP	1.05302	0.969
39DAP/27DAP	0.62696
41DAP/39DAP	1.00389	1
42DAP/41DAP	1.07843	1
43DAP/42DAP	1.2097
47DAP/43DAP	1.22066	0.853
52DAP/47DAP	0.71155	0.261
57DAP/52DAP	1.48608	0.507
57DAP/7DAP	1.01367	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12189	0.119
17DAP/reference	1.36967	0.007
27DAP/reference	1.48018	0.008
39DAP/reference	1.3555	0.009
41DAP/reference	1.3676	0.012
42DAP/reference	1.38217	0.011
43DAP/reference	1.36072	0.007
47DAP/reference	1.09011	0.7
52DAP/reference	1.28994	0.017
57DAP/reference	1.34118	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88369	0.231
17DAP/reference	0.83939	0.006
27DAP/reference	0.90895	0.292
39DAP/reference	1.04842	0.401
41DAP/reference	1.0789	0.48
42DAP/reference	1.06295	0.777
43DAP/reference	1.11298	0.362
47DAP/reference	0.97513	0.379
52DAP/reference	1.08636	0.24
57DAP/reference	0.94232	0.338

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.40858	0.016
17DAP/reference	1.20635	0.394
27DAP/reference	1.82184	0.018
39DAP/reference	1.40737	0.011
41DAP/reference	1.26442	0.017
42DAP/reference	1.16613	0.251
43DAP/reference	1.19006	0.241
47DAP/reference	1.02064	0.877
52DAP/reference	1.37511	0.094
57DAP/reference	1.19056	0.021

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.15425	0.966
26DAP/20DAP	0.72138	0.317
34DAP/26DAP	1.15897	1
51DAP/34DAP	1.96255	0.746
52DAP/51DAP	0.668	1
53DAP/52DAP	0.86223	0.64
55DAP/53DAP	0.96329	0.807
57DAP/55DAP	0.8492	0.437
62DAP/57DAP	1.04388	0.902
68DAP/62DAP	1.39942	0.024
68DAP/14DAP	1.71426	0.029

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.56786	0.018

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.99653	0.715
Immature Eggplant/Mature Eggplant	1.18203	0.462
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	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	1.13476
12-4/M82	1.1919
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	0.92939
3-2/M82	0.67687
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	0.26859
5-3/M82	0.94809
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.01536
9-3-2/M82	0.95585

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.83722	0.321
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.66766	1
IL7-3/WTpooled	0.83995
IL12-4/WTpooled	0.62842	0.71
IL1-4/WTpooled	1.08652	1
WT/WTpooled	1.12465	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03716	0.914
DC3000/delta hrp 6h	0.78301	0.942
DC3000/delta hrp 12h	1.00263	1
DC3000/delta hrp 24h	0.96434	0.761

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	1.02239	0.254
Exp 36h	0.6646	0.321
Exp 60h	0.80835	0.257

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	N/A	N/A
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)	1.01846	1
transgenic ySAMdc/azygous control (breaker)	1.09677	1
transgenic ySAMdc/azygous control (red)	0.90379	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02677	0.525

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.99363	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.08444	1
Manapal/WT (break)	1.07071	1
Manapal/WT (red)	1.15909	1