Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.12.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9591	0.728
27DAP/17DAP	1.01994	0.92
39DAP/27DAP	0.93239	0.594
41DAP/39DAP	3.08778	0.118
42DAP/41DAP	3.38335	0.028
43DAP/42DAP	8.66494	0.016
47DAP/43DAP	1.69991	0.23
52DAP/47DAP	0.38274	0.034
57DAP/52DAP	0.50894	0.462

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.42481	0.025
17DAP/reference	0.32956	0.008
27DAP/reference	0.54843	0.03
39DAP/reference	0.72235	0.136
41DAP/reference	0.57371	0.039
42DAP/reference	1.87394	0.011
43DAP/reference	7.89143	0.006
47DAP/reference	9.67938	0.001
52DAP/reference	2.55551	0.017
57DAP/reference	2.15936	0.023

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03842	0.826
27DAP/17DAP	1.01798	0.969
39DAP/27DAP	0.9875	0.887
41DAP/39DAP	1.02026	1
42DAP/41DAP	2.12261	0.023
43DAP/42DAP	8.87173	0.013
47DAP/43DAP	1.90507	0.017
52DAP/47DAP	1.34062
57DAP/52DAP	0.52102	0.049
57DAP/7DAP	3.03978	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10142	1
17DAP/reference	1.17357	0.014
27DAP/reference	1.71085	0.008
39DAP/reference	2.7584	0.005
41DAP/reference	1.3029	0.117
42DAP/reference	2.72389	0.006
43DAP/reference	2.83205	0.007
47DAP/reference	1.6677	0.618
52DAP/reference	2.20507	0.009
57DAP/reference	1.67291	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.53771	0.012
17DAP/reference	0.41638	0.003
27DAP/reference	0.57664	0.014
39DAP/reference	0.49244	0.032
41DAP/reference	0.72643	0.018
42DAP/reference	0.7542	0.046
43DAP/reference	0.76057	0.09
47DAP/reference	0.65496	0.016
52DAP/reference	0.46468	0.004
57DAP/reference	0.29332	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09897	0.338
17DAP/reference	1.00098	0.681
27DAP/reference	2.11224	0.081
39DAP/reference	2.00358	0.039
41DAP/reference	1.58405	0.056
42DAP/reference	2.17625	0.007
43DAP/reference	5.63661	0.013
47DAP/reference	9.29041	0.005
52DAP/reference	2.87119	0.038
57DAP/reference	1.30713	0.354

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93085	1
26DAP/20DAP	1.18844	0.281
34DAP/26DAP	1.1414	1
51DAP/34DAP	0.88412	0.492
52DAP/51DAP	1.07945	0.626
53DAP/52DAP	1.86696	0.038
55DAP/53DAP	1.37822	0.193
57DAP/55DAP	0.9399	0.709
62DAP/57DAP	0.06698	0.002
68DAP/62DAP	2.40022	0.095
68DAP/14DAP	1.50852	0.636

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.49324	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	0.0834	0.019
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.10698	0.224
Mature Eggplant/Ripe Tomato	0.02046	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	2.67067	0.505
1-1-2/M82	2.89064	1
12-2/M82	0.59288	0.692
12-4/M82	4.88416	1
1-3/M82	3.83239	0.255
2-1-1/M82	1.13245	1
2-1/M82	0.61494	0.325
2-6/M82	1.95526	0.364
3-2/M82	1.55388	0.717
4-1-1/M82	2.48456	0.977
4-1/M82	15.1466	0.853
4-3-2/M82	2.0032
4-3/M82	1.79452	0.268
5-3/M82	0.7444	1
6-2/M82	5.87139	0.235
6-3/M82	1.37401	1
7-1/M82	0.9238	1
7-2/M82	1.87455	0.302
9-3-2/M82	3.30856	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	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	0.97524	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96711	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.04325	1
DC3000/delta hrp 24h	0.92814	0.438

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.84559	0.077
DC3000 delta B/DC3000 delta AB	0.9641	0.745

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
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	0.99055	1
Var 0h	0.51283	1
Var 12h I row2-row1	0.91363	0.338
Var 12h NI row2-row1	1.08774	1
Var 36h I row2-row1	0.96927	1
Var 36h NI row2-row1	3.88807	1
Var 60h I row2-row1	1.05416	1
Var 60h NI row2-row1	1.05629	1
Time course 0hI-0hNI	0.96166	0.777
Time course 12hI-12hNI	0.99202	1
Time course 36hI-36hNI	1.05589	0.101
Time course 60hI-60hNI	0.48801	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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	0.54223	0.142
transgenic ySAMdc/azygous control (red)	0.98226	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97066	0.237

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.14195	1
Manapal/WT (red)	0.72983	0.274