Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.18.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.3428	0.348
27DAP/17DAP	1.46134	0.714
39DAP/27DAP	2.70682	0.077
41DAP/39DAP	0.97756	0.862
42DAP/41DAP	0.5917	0.397
43DAP/42DAP	1.28067	0.746
47DAP/43DAP	1.18503	0.469
52DAP/47DAP	0.81145	0.539
57DAP/52DAP	1.06615	0.988

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0034	1
17DAP/reference	1.01005	0.957
27DAP/reference	1.0089	1
39DAP/reference	0.97502	0.704
41DAP/reference	0.84961	0.154
42DAP/reference	0.96167	0.188
43DAP/reference	1.13651	0.34
47DAP/reference	1.03438	0.817
52DAP/reference	1.09433	0.407
57DAP/reference	0.95637	0.262

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.71363	0.053
27DAP/17DAP	1.30033	0.18
39DAP/27DAP	1.17455	0.347
41DAP/39DAP	0.83129	0.42
42DAP/41DAP	0.94864	0.712
43DAP/42DAP	1.18781	0.134
47DAP/43DAP	1.02197	0.948
52DAP/47DAP	1.00831	0.975
57DAP/52DAP	0.90468	0.48
57DAP/7DAP	1.3615	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.25773	0.029
17DAP/reference	3.34846	0.006
27DAP/reference	3.97359	0.008
39DAP/reference	5.70644	0.005
41DAP/reference	5.95137	0.009
42DAP/reference	7.79645	0.006
43DAP/reference	5.30388	0.007
47DAP/reference	2.63619	0.057
52DAP/reference	2.87927	0.007
57DAP/reference	2.67995	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14559	1
17DAP/reference	0.6671	0.01
27DAP/reference	1.10006	0.463
39DAP/reference	1.23931	0.247
41DAP/reference	1.72238	0.005
42DAP/reference	1.11217	0.5
43DAP/reference	0.78404	0.092
47DAP/reference	1.045	0.749
52DAP/reference	0.80956	0.027
57DAP/reference	1.02508	0.887

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.37241	0.076
17DAP/reference	1.54012	0.631
27DAP/reference	3.04104	0.019
39DAP/reference	4.03686	0.011
41DAP/reference	2.61832	0.009
42DAP/reference	3.80706	0.007
43DAP/reference	2.03	0.026
47DAP/reference	1.16025	0.443
52DAP/reference	4.13055	0.039
57DAP/reference	3.37666	0.007

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.88621	0.997
26DAP/20DAP	1.05416	1
34DAP/26DAP	1.06746	1
51DAP/34DAP	1.03145	0.993
52DAP/51DAP	1.07616	0.776
53DAP/52DAP	2.11679	0.041
55DAP/53DAP	0.99872	0.925
57DAP/55DAP	0.63022	0.043
62DAP/57DAP	0.58039	0.005
68DAP/62DAP	1.79672	0.682
68DAP/14DAP	1.0531	0.826

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.87481	0.304

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.13244	0.068
Mature Green Tomato/Ripe Tomato	0.86563	0.487
Immature Eggplant/Mature Eggplant	10.5704	0.05
Ripe Pepper/Ripe Tomato	0.82644	0.224
Mature Eggplant/Ripe Tomato	0.23658	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96763	0.961
1-1-2/M82	1.07201	1
12-2/M82	0.79787	0.661
12-4/M82	0.99458	1
1-3/M82	0.96322
2-1-1/M82	1.19472	0.439
2-1/M82	1.35032
2-6/M82	N/A	N/A
3-2/M82	1.13839	0.84
4-1-1/M82	1.15714	1
4-1/M82	1.00212	1
4-3-2/M82	0.80409
4-3/M82	0.81982	1
5-3/M82	1.50069	0.427
6-2/M82	0.79768	0.481
6-3/M82	0.94695	0.982
7-1/M82	1.1239	0.598
7-2/M82	0.99191	1
9-3-2/M82	1.44589	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.06983	1
IL2-6/WTpooled	0.88176	1
IL7-5/WTpooled	0.73926	1
IL7-3/WTpooled	0.78761	1
IL12-4/WTpooled	1.28298	0.557
IL1-4/WTpooled	1.0987	1
WT/WTpooled	1.00526	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	0.96084	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92522	0.868
DC3000/delta hrp 6h	0.99856	0.95
DC3000/delta hrp 12h	1.0691	1
DC3000/delta hrp 24h	1.5927	0.039

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.41134	0.046
DC3000 delta B/DC3000 delta AB	2.01063	0.118

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.3477	1
Exp 36h	2.09352	0.489
Exp 60h	1.9455	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	1.25538	1
Var 0h	0.84772	1
Var 12h I row2-row1	0.90715	0.705
Var 12h NI row2-row1	1.24789	0.649
Var 36h I row2-row1	0.96969	1
Var 36h NI row2-row1	0.84365	0.645
Var 60h I row2-row1	0.95882	0.832
Var 60h NI row2-row1	0.81335	0.756
Time course 0hI-0hNI	1.19275	0.377
Time course 12hI-12hNI	1.24613	0.02
Time course 36hI-36hNI	1.89284	0.007
Time course 60hI-60hNI	6.70828	0.008

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)	1.19492	0.571
transgenic ySAMdc/azygous control (breaker)	1.09698	1
transgenic ySAMdc/azygous control (red)	0.98151	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06491	0.148

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88354	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.64424	0.105
Manapal/WT (break)	1.12841	1
Manapal/WT (red)	1.28993	0.413