Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.10.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.29104	0.166
27DAP/17DAP	0.76539	0.366
39DAP/27DAP	1.22348	1
41DAP/39DAP	1.24364	0.701
42DAP/41DAP	1.40072	0.767
43DAP/42DAP	1.01688	1
47DAP/43DAP	1.13809	0.825
52DAP/47DAP	1.13277	0.879
57DAP/52DAP	1.10152	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.72454	0.078
17DAP/reference	0.43191	0.008
27DAP/reference	0.44904	0.015
39DAP/reference	0.43501	0.016
41DAP/reference	0.21284	0.008
42DAP/reference	0.31791	0.001
43DAP/reference	0.22058	0.012
47DAP/reference	0.18405	0.001
52DAP/reference	0.21283	0.013
57DAP/reference	0.25964	0.006

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.45504	0.189
27DAP/17DAP	0.76805	0.172
39DAP/27DAP	0.66365	0.038
41DAP/39DAP	1.03523	0.909
42DAP/41DAP	0.98131	0.819
43DAP/42DAP	0.77031	0.097
47DAP/43DAP	0.86465	0.037
52DAP/47DAP	1.49484	0.111
57DAP/52DAP	1.35358	0.108
57DAP/7DAP	1.13576	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12529	0.385
17DAP/reference	0.85105	0.031
27DAP/reference	0.53824	0.01
39DAP/reference	0.41265	0.011
41DAP/reference	0.34057	0.009
42DAP/reference	0.32159	0.01
43DAP/reference	0.25872	0.009
47DAP/reference	0.24354	0.03
52DAP/reference	0.37283	0.009
57DAP/reference	0.36143	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.41473	0.007
17DAP/reference	0.45258	0.009
27DAP/reference	0.59046	0.048
39DAP/reference	0.29445	0.01
41DAP/reference	0.33243	0.005
42DAP/reference	0.31534	0.01
43DAP/reference	0.14536	0.002
47DAP/reference	0.23675	0.008
52DAP/reference	0.21012	0.004
57DAP/reference	0.07754	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.46543	0.015
17DAP/reference	2.23754	0.228
27DAP/reference	1.57109	0.026
39DAP/reference	1.26522	0.026
41DAP/reference	0.74395	0.037
42DAP/reference	0.52751	0.018
43DAP/reference	0.57808	0.016
47DAP/reference	0.19987	0.004
52DAP/reference	0.36045	0.068
57DAP/reference	1.57969	0.175

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08171	1
26DAP/20DAP	1.13896	0.581
34DAP/26DAP	1.1857	1
51DAP/34DAP	0.70818	0.066
52DAP/51DAP	1.1863	0.313
53DAP/52DAP	0.85716	0.245
55DAP/53DAP	1.16228	0.247
57DAP/55DAP	0.67859	0.066
62DAP/57DAP	2.65525	0.217
68DAP/62DAP	1.86276	0.278
68DAP/14DAP	0.55382	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.64916	0.031

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.97242	0.058
Mature Green Tomato/Ripe Tomato	2.14865	0.07
Immature Eggplant/Mature Eggplant	0.47494	0.062
Ripe Pepper/Ripe Tomato	40.8941	0.258
Mature Eggplant/Ripe Tomato	76.7838	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06415	1
1-1-2/M82	0.84979
12-2/M82	N/A	N/A
12-4/M82	1.14528
1-3/M82	0.73706	0.378
2-1-1/M82	0.76206
2-1/M82	N/A	N/A
2-6/M82	0.93632	1
3-2/M82	N/A	N/A
4-1-1/M82	1.03789	1
4-1/M82	1.7589
4-3-2/M82	1.06406
4-3/M82	N/A	N/A
5-3/M82	1.09216	0.572
6-2/M82	0.69182	1
6-3/M82	0.96407
7-1/M82	N/A	N/A
7-2/M82	0.89622	0.881
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	1.09372	0.659
IL7-5/WTpooled	0.79006
IL7-3/WTpooled	0.91129	0.418
IL12-4/WTpooled	0.7184	0.71
IL1-4/WTpooled	1.00079	1
WT/WTpooled	1.00348	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	0.95077	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01483	0.921
DC3000/delta hrp 6h	0.8369	0.95
DC3000/delta hrp 12h	1.00719	1
DC3000/delta hrp 24h	1.01574	0.821

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.51128	0.023
DC3000 delta B/DC3000 delta AB	0.46891	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97528	1
Exp 36h	1.06318	1
Exp 60h	1.12955	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96943	1
Var 0h	1.58728	0.98
Var 12h I row2-row1	0.89235	0.338
Var 12h NI row2-row1	1.01502	1
Var 36h I row2-row1	0.83694	0.805
Var 36h NI row2-row1	0.98987	0.852
Var 60h I row2-row1	1.54813	0.562
Var 60h NI row2-row1	1.0028	1
Time course 0hI-0hNI	0.97402	0.801
Time course 12hI-12hNI	1.01644	0.818
Time course 36hI-36hNI	1.08393	0.07
Time course 60hI-60hNI	0.45934	0.026

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)	1.19766	0.699
transgenic ySAMdc/azygous control (breaker)	3.92485	0.161
transgenic ySAMdc/azygous control (red)	1.48059	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.52021	0.074

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.85853	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	19.2826	0.083
Manapal/WT (break)	15.7486	0.123
Manapal/WT (red)	4.06368	0.413