Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.3.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.32549	0.038
27DAP/17DAP	1.24885	0.761
39DAP/27DAP	1.87587	0.068
41DAP/39DAP	0.77529	0.24
42DAP/41DAP	0.99584	1
43DAP/42DAP	1.16471	1
47DAP/43DAP	1.01442	1
52DAP/47DAP	1.1331	0.806
57DAP/52DAP	1.67579	0.787

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.66778	0.025
17DAP/reference	1.00267	0.957
27DAP/reference	1.04297	0.797
39DAP/reference	1.02522	0.603
41DAP/reference	1.228	0.552
42DAP/reference	0.96228	0.413
43DAP/reference	1.28678
47DAP/reference	1.36811	0.01
52DAP/reference	2.04849	0.018
57DAP/reference	1.42459

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.0263	0.036
27DAP/17DAP	1.03291	0.942
39DAP/27DAP	1.02419	0.811
41DAP/39DAP	1.14392	1
42DAP/41DAP	1.18101	0.55
43DAP/42DAP	0.80673	0.022
47DAP/43DAP	0.94362	0.647
52DAP/47DAP	1.14872	0.532
57DAP/52DAP	1.05431	0.858
57DAP/7DAP	1.59198	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14481	0.193
17DAP/reference	1.67108	0.006
27DAP/reference	1.76312	0.007
39DAP/reference	2.20239	0.005
41DAP/reference	1.70855	0.009
42DAP/reference	1.86511	0.006
43DAP/reference	1.78699	0.006
47DAP/reference	1.86493	0.016
52DAP/reference	1.98805	0.007
57DAP/reference	1.89729	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.62489	0.009
17DAP/reference	1.0293	1
27DAP/reference	1.33768	0.02
39DAP/reference	1.46546	0.011
41DAP/reference	1.2648	0.046
42DAP/reference	1.29733	0.074
43DAP/reference	0.85956	0.191
47DAP/reference	1.13762	0.089
52DAP/reference	1.01318	1
57DAP/reference	0.79496	0.085

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83686	0.057
17DAP/reference	1.01437	0.727
27DAP/reference	2.00674	0.023
39DAP/reference	1.89995	0.014
41DAP/reference	1.63059	0.006
42DAP/reference	1.37627	0.021
43DAP/reference	1.62864	0.031
47DAP/reference	1.07568	1
52DAP/reference	1.82249	0.056
57DAP/reference	3.05534	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.15524	0.966
26DAP/20DAP	1.30152	0.385
34DAP/26DAP	0.78316	0.103
51DAP/34DAP	1.75239	0.037
52DAP/51DAP	0.62002	0.079
53DAP/52DAP	1.26485	0.398
55DAP/53DAP	0.72695	0.05
57DAP/55DAP	1.4593	0.214
62DAP/57DAP	1.4785	0.445
68DAP/62DAP	1.17609	0.831
68DAP/14DAP	1.62244	0.087

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.61636	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.61858	0.141
Mature Green Tomato/Ripe Tomato	1.05101	0.69
Immature Eggplant/Mature Eggplant	0.89303	0.223
Ripe Pepper/Ripe Tomato	0.86426	0.224
Mature Eggplant/Ripe Tomato	0.70356	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.11709	1
1-1-2/M82	1.16617	1
12-2/M82	0.476	0.678
12-4/M82	1.21589	0.655
1-3/M82	1.94895
2-1-1/M82	1.23564	0.764
2-1/M82	0.98333	1
2-6/M82	0.94153	1
3-2/M82	2.55033
4-1-1/M82	1.93315	0.938
4-1/M82	2.40742	0.512
4-3-2/M82	1.08151
4-3/M82	1.19959	1
5-3/M82	1.05135	1
6-2/M82	1.13826	1
6-3/M82	1.24153	1
7-1/M82	1.30114	0.598
7-2/M82	1.14277	1
9-3-2/M82	1.12795	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.86355
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	1.0511	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92939	1
DC3000/delta hrp 6h	0.9588	0.95
DC3000/delta hrp 12h	0.99826	1
DC3000/delta hrp 24h	0.68467	0.076

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.37526	0.025
DC3000 delta B/DC3000 delta AB	0.28769	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.87297	0.328
Exp 36h	0.79125	0.41
Exp 60h	0.68893	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02065	1
Var 0h	1.2387	0.98
Var 12h I row2-row1	0.78788	0.338
Var 12h NI row2-row1	0.6211	0.33
Var 36h I row2-row1	0.70583	1
Var 36h NI row2-row1	2.11561	0.482
Var 60h I row2-row1	1.31482
Var 60h NI row2-row1	1.60038	0.586
Time course 0hI-0hNI	0.67891	0.044
Time course 12hI-12hNI	1.06244	0.738
Time course 36hI-36hNI	0.86528	0.048
Time course 60hI-60hNI	0.07412	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)	0.94166	0.454
transgenic ySAMdc/azygous control (breaker)	0.54636	0.139
transgenic ySAMdc/azygous control (red)	0.97615	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.29925	0.247

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.26284	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.58085	0.172
Manapal/WT (break)	0.59556	0.299
Manapal/WT (red)	0.94352	0.503