Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.11.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.23448	0.681
27DAP/17DAP	1.20973	0.809
39DAP/27DAP	1.14771	0.755
41DAP/39DAP	1.23306	0.569
42DAP/41DAP	0.93759	1
43DAP/42DAP	0.86887	0.556
47DAP/43DAP	1.43577	0.463
52DAP/47DAP	0.99893	0.845
57DAP/52DAP	1.21393	0.853

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.32636
17DAP/reference	N/A	N/A
27DAP/reference	N/A	N/A
39DAP/reference	1.00356	0.975
41DAP/reference	1.31729	0.587
42DAP/reference	1.36077	0.093
43DAP/reference	0.31428
47DAP/reference	0.55775	0.174
52DAP/reference	N/A	N/A
57DAP/reference	2.25733

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16052	0.213
27DAP/17DAP	0.76975	0.241
39DAP/27DAP	1.39686	0.128
41DAP/39DAP	0.90092	0.321
42DAP/41DAP	1.02477	0.935
43DAP/42DAP	0.989	0.902
47DAP/43DAP	1.3422	0.018
52DAP/47DAP	1.00664	1
57DAP/52DAP	0.91138	0.473
57DAP/7DAP	0.99851	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93304	0.146
17DAP/reference	0.93892	0.064
27DAP/reference	0.88097	0.048
39DAP/reference	0.92825	0.146
41DAP/reference	0.99691	0.778
42DAP/reference	0.7891	0.026
43DAP/reference	0.89308	0.151
47DAP/reference	0.91025	0.168
52DAP/reference	0.99591	0.74
57DAP/reference	1.22052	0.07

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02572	0.885
17DAP/reference	1.05996	0.471
27DAP/reference	0.8618	0.09
39DAP/reference	1.0561	0.824
41DAP/reference	0.74879	0.06
42DAP/reference	0.86316	0.392
43DAP/reference	0.8555	0.206
47DAP/reference	N/A	N/A
52DAP/reference	0.96314	0.28
57DAP/reference	0.97461	0.581

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87815	0.057
17DAP/reference	0.97762	0.658
27DAP/reference	0.81512	0.035
39DAP/reference	0.86215	0.012
41DAP/reference	0.88743	0.167
42DAP/reference	0.79083	0.014
43DAP/reference	0.85576	0.068
47DAP/reference	0.92362	0.259
52DAP/reference	0.89839	0.238
57DAP/reference	0.97836	0.543

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01126	1
26DAP/20DAP	0.97889	1
34DAP/26DAP	1.03632	1
51DAP/34DAP	0.95804	0.737
52DAP/51DAP	0.93375	1
53DAP/52DAP	1.03585	0.921
55DAP/53DAP	1.26492	0.162
57DAP/55DAP	1.02963	0.927
62DAP/57DAP	1.15062	0.445
68DAP/62DAP	1.09038	0.899
68DAP/14DAP	0.89499	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.18472	0.049

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.53681	0.182
Mature Green Tomato/Ripe Tomato	0.22171
Immature Eggplant/Mature Eggplant	10.7392	0.05
Ripe Pepper/Ripe Tomato	0.71677	1
Mature Eggplant/Ripe Tomato	0.90514	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.07927	0.742
1-1-2/M82	0.95663	1
12-2/M82	1.16987	1
12-4/M82	0.81241	1
1-3/M82	1.18154
2-1-1/M82	2.28126
2-1/M82	2.18939	0.345
2-6/M82	0.95066	1
3-2/M82	0.71009	0.752
4-1-1/M82	0.94692	1
4-1/M82	0.96853
4-3-2/M82	1.34619	0.508
4-3/M82	1.21047	1
5-3/M82	1.28531	0.496
6-2/M82	0.90004	1
6-3/M82	1.05511	1
7-1/M82	0.94859	1
7-2/M82	1.02747	1
9-3-2/M82	0.87178	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.21783	1
IL2-6/WTpooled	1.11486	0.659
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.76045	0.298
IL12-4/WTpooled	0.99456	1
IL1-4/WTpooled	0.97718	1
WT/WTpooled	1.07584	0.999

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	1.39173	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.80291	0.849
DC3000/delta hrp 6h	1.41448	1
DC3000/delta hrp 12h	1.03398	1
DC3000/delta hrp 24h	1.49306	0.038

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.15786	0.076
DC3000 delta B/DC3000 delta AB	1.37821	0.141

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.18128	1
Exp 36h	1.3931	0.489
Exp 60h	1.56534	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96302	1
Var 0h	0.48922	0.933
Var 12h I row2-row1	0.98891	0.948
Var 12h NI row2-row1	0.99108	1
Var 36h I row2-row1	1.04602	1
Var 36h NI row2-row1	0.93852	0.522
Var 60h I row2-row1	0.92485	0.439
Var 60h NI row2-row1	0.94439	0.932
Time course 0hI-0hNI	1.00192	1
Time course 12hI-12hNI	0.977	0.624
Time course 36hI-36hNI	1.18048	0.799
Time course 60hI-60hNI	3.2035	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)	0.83558	0.289
transgenic ySAMdc/azygous control (breaker)	1.33511	0.248
transgenic ySAMdc/azygous control (red)	1.01841	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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)	0.68591	1
Manapal/WT (break)	1.0939	1
Manapal/WT (red)	0.87004	0.503