Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.4.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98107	0.811
27DAP/17DAP	0.85088	0.621
39DAP/27DAP	1.07074	0.974
41DAP/39DAP	1.48604	0.483
42DAP/41DAP	1.04383	1
43DAP/42DAP	1.03423	0.945
47DAP/43DAP	1.12352	0.856
52DAP/47DAP	1.23934	0.608
57DAP/52DAP	1.16657	0.952

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78352	0.055
17DAP/reference	0.84959	0.038
27DAP/reference	0.92332	0.265
39DAP/reference	0.91645	0.254
41DAP/reference	0.88986	0.026
42DAP/reference	0.88516	0.029
43DAP/reference	0.98732	0.805
47DAP/reference	0.86919	0.09
52DAP/reference	0.98536	0.564
57DAP/reference	1.12937	0.105

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81742	0.299
27DAP/17DAP	1.20229	0.407
39DAP/27DAP	1.04039	0.718
41DAP/39DAP	1.09127	0.876
42DAP/41DAP	1.10742	0.947
43DAP/42DAP	1.4239	0.031
47DAP/43DAP	1.03894	0.93
52DAP/47DAP	0.9745	0.917
57DAP/52DAP	1.02826	1
57DAP/7DAP	1.20171	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99939	0.758
17DAP/reference	1.23435	0.627
27DAP/reference	0.84983	0.088
39DAP/reference	1.02857	0.96
41DAP/reference	0.7844	0.026
42DAP/reference	1.13384	0.534
43DAP/reference	0.98546	0.527
47DAP/reference	0.97963	0.671
52DAP/reference	0.90871	0.163
57DAP/reference	0.99866	0.629

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77045	0.053
17DAP/reference	0.85704	0.011
27DAP/reference	0.88073	0.111
39DAP/reference	0.90297	0.178
41DAP/reference	0.85802	0.145
42DAP/reference	0.88382	0.081
43DAP/reference	1.04134	0.831
47DAP/reference	1.06379	0.513
52DAP/reference	0.99965	0.713
57DAP/reference	0.76721	0.05

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86545	0.29
17DAP/reference	0.98469	0.739
27DAP/reference	1.01347	1
39DAP/reference	0.99198	0.755
41DAP/reference	0.89948	0.077
42DAP/reference	0.68159	0.032
43DAP/reference	0.92449	0.348
47DAP/reference	0.93089	0.315
52DAP/reference	0.76143	0.055
57DAP/reference	0.85498	0.171

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.31488	0.966
26DAP/20DAP	1.02338	1
34DAP/26DAP	1.05311	0.304
51DAP/34DAP	0.93838	0.747
52DAP/51DAP	1.38233	0.092
53DAP/52DAP	1.24014	0.537
55DAP/53DAP	1.04192	0.964
57DAP/55DAP	0.75578	0.19
62DAP/57DAP	0.91541	0.681
68DAP/62DAP	1.89013	0.44
68DAP/14DAP	1.2042	0.694

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.98322	0.635

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.7349	0.256
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.51888
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	0.96981
12-2/M82	N/A	N/A
12-4/M82	0.88261
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	N/A	N/A
3-2/M82	N/A	N/A
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	N/A	N/A
5-3/M82	1.02518
6-2/M82	N/A	N/A
6-3/M82	0.89121
7-1/M82	0.8481
7-2/M82	N/A	N/A
9-3-2/M82	0.92144

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	2.40427	0.584
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.09094	1
IL12-4/WTpooled	1.03492	1
IL1-4/WTpooled	0.91449
WT/WTpooled	1.02169	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	0.71225	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06125	0.629
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.06261	1
DC3000/delta hrp 24h	1.27038	0.397

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	1.09459	1
Exp 36h	N/A	N/A
Exp 60h	0.99465	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01097	1
Var 0h	1.14002	1
Var 12h I row2-row1	0.98433	1
Var 12h NI row2-row1	0.9891	1
Var 36h I row2-row1	1.14132	1
Var 36h NI row2-row1	0.98038	0.852
Var 60h I row2-row1	1.01474
Var 60h NI row2-row1	1.01982	1
Time course 0hI-0hNI	1.03731	0.852
Time course 12hI-12hNI	1.03269	0.741
Time course 36hI-36hNI	0.99051	0.68
Time course 60hI-60hNI	0.69518	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)	0.94118	0.567
transgenic ySAMdc/azygous control (breaker)	0.87554	0.142
transgenic ySAMdc/azygous control (red)	1.04249	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03539	0.135

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01368	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.9845	1
Manapal/WT (break)	1.11518	1
Manapal/WT (red)	0.8217	0.424