Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.17.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.54165	0.443
27DAP/17DAP	0.73683	0.149
39DAP/27DAP	1.30696	0.677
41DAP/39DAP	1.49818	0.268
42DAP/41DAP	1.39395	0.114
43DAP/42DAP	1.90309	0.045
47DAP/43DAP	1.93406	0.198
52DAP/47DAP	1.54976	0.349
57DAP/52DAP	1.09694	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06671	0.928
17DAP/reference	0.95591	0.536
27DAP/reference	1.01769	1
39DAP/reference	1.69621	0.04
41DAP/reference	1.44304	0.062
42DAP/reference	2.6882	0.001
43DAP/reference	2.63503	0.007
47DAP/reference	6.88889	0.001
52DAP/reference	3.3617	0.007
57DAP/reference	3.5567	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.40275	0.064
27DAP/17DAP	1.64406	0.038
39DAP/27DAP	2.7298	0.046
41DAP/39DAP	0.2813	0.013
42DAP/41DAP	6.38167	0.002
43DAP/42DAP	3.94776	0.013
47DAP/43DAP	1.05031	0.963
52DAP/47DAP	1.46513	0.36
57DAP/52DAP	1.28932	0.659
57DAP/7DAP	7.65925	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.46835	0.058
17DAP/reference	0.41809	0.011
27DAP/reference	0.63436	0.01
39DAP/reference	1.05265	0.511
41DAP/reference	0.66937	0.039
42DAP/reference	0.84141	0.09
43DAP/reference	0.88067	0.23
47DAP/reference	1.63363	0.032
52DAP/reference	0.90403	0.179
57DAP/reference	0.49532	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.62838	0.064
17DAP/reference	0.82118	0.245
27DAP/reference	0.89903	0.327
39DAP/reference	1.07835	0.401
41DAP/reference	1.19825	0.024
42DAP/reference	1.26358	0.096
43DAP/reference	0.94424	0.45
47DAP/reference	1.1957	0.527
52DAP/reference	0.79209	0.072
57DAP/reference	0.81785	0.073

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.45084	0.032
17DAP/reference	1.07675	0.488
27DAP/reference	0.49846	0.026
39DAP/reference	0.85798	0.05
41DAP/reference	0.70192	0.035
42DAP/reference	2.29726	0.006
43DAP/reference	2.51772	0.007
47DAP/reference	2.26916	0.007
52DAP/reference	1.82903	0.036
57DAP/reference	1.58698	0.018

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.48292	1
26DAP/20DAP	0.70877	0.512
34DAP/26DAP	1.22969	1
51DAP/34DAP	8.67272	0.019
52DAP/51DAP	0.63898	0.151
53DAP/52DAP	11.2632	0.016
55DAP/53DAP	1.06283	0.681
57DAP/55DAP	0.49792	0.02
62DAP/57DAP	0.34856	0.005
68DAP/62DAP	1.3483	0.616
68DAP/14DAP	0.67031

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.43758	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.14841	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.19194	0.224
Mature Eggplant/Ripe Tomato	0.1676	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0033	1
1-1-2/M82	1.06238	1
12-2/M82	1.29374	1
12-4/M82	0.9806	0.619
1-3/M82	0.86529	1
2-1-1/M82	0.84516	0.784
2-1/M82	0.97702	1
2-6/M82	0.95469	1
3-2/M82	0.06673	0.125
4-1-1/M82	0.91504	1
4-1/M82	1.25447	1
4-3-2/M82	0.85327	1
4-3/M82	0.93878	1
5-3/M82	0.86908	1
6-2/M82	1.01654	1
6-3/M82	1.0292	1
7-1/M82	0.83807	0.803
7-2/M82	1.06397	0.385
9-3-2/M82	1.53177	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.23678
IL12-4/WTpooled	1.00831	1
IL1-4/WTpooled	1.39202
WT/WTpooled	0.93767	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	1.78504	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00949	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.19199
DC3000/delta hrp 24h	0.75135	0.045

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.33406
DC3000 delta B/DC3000 delta AB	1.19256	0.389

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.20527	1
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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	1.10665	0.98
Var 12h I row2-row1	1.56253	0.125
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	1.00863
Var 36h NI row2-row1	0.75985
Var 60h I row2-row1	0.49441
Var 60h NI row2-row1	0.74789	0.38
Time course 0hI-0hNI	1.21472
Time course 12hI-12hNI	1.15434
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	4.59921

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)	1.42035	0.3
transgenic ySAMdc/azygous control (breaker)	0.52305	0.142
transgenic ySAMdc/azygous control (red)	0.76669	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02144	0.155

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.1954	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.65975	1
Manapal/WT (break)	1.24934	1
Manapal/WT (red)	0.86648	0.424