Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.6.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97162	0.76
27DAP/17DAP	1.12672	0.836
39DAP/27DAP	1.14889	0.804
41DAP/39DAP	1.28989	0.584
42DAP/41DAP	1.07411	1
43DAP/42DAP	0.8284	0.589
47DAP/43DAP	1.29582	0.463
52DAP/47DAP	1.22376	0.739
57DAP/52DAP	1.16453	0.964

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91588	0.3
17DAP/reference	1.01086	0.957
27DAP/reference	1.15374	0.426
39DAP/reference	1.07574	0.664
41DAP/reference	1.01206	1
42DAP/reference	1.0593	0.782
43DAP/reference	1.05309	0.646
47DAP/reference	1.19325	0.175
52DAP/reference	1.05989	1
57DAP/reference	1.13161	0.511

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01575	1
27DAP/17DAP	0.80089	0.135
39DAP/27DAP	1.13446	0.534
41DAP/39DAP	1.1216	0.748
42DAP/41DAP	0.98239	0.777
43DAP/42DAP	1.09979	0.513
47DAP/43DAP	1.01514	0.957
52DAP/47DAP	1.14054	0.568
57DAP/52DAP	0.93941	0.384
57DAP/7DAP	1.17808	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76171	0.065
17DAP/reference	0.73311	0.011
27DAP/reference	0.71366	0.01
39DAP/reference	0.72944	0.011
41DAP/reference	0.74835	0.017
42DAP/reference	0.64588	0.01
43DAP/reference	0.67377	0.012
47DAP/reference	0.94748	0.504
52DAP/reference	0.68498	0.012
57DAP/reference	0.69894	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82955	0.019
17DAP/reference	0.71925	0.024
27DAP/reference	0.82474	0.203
39DAP/reference	0.75328	0.028
41DAP/reference	0.80505	0.094
42DAP/reference	0.75386	0.021
43DAP/reference	0.97084	0.478
47DAP/reference	1.0041	0.833
52DAP/reference	0.69391	0.008
57DAP/reference	0.77903	0.035

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84707	0.054
17DAP/reference	0.84831	0.231
27DAP/reference	0.78669	0.043
39DAP/reference	0.70474	0.01
41DAP/reference	0.83246	0.025
42DAP/reference	0.69821	0.02
43DAP/reference	0.72665	0.046
47DAP/reference	0.7364	0.023
52DAP/reference	0.80205	0.247
57DAP/reference	0.91895	0.082

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09331	0.966
26DAP/20DAP	0.74549	0.317
34DAP/26DAP	1.114	1
51DAP/34DAP	1.17019	0.565
52DAP/51DAP	1.13843	0.42
53DAP/52DAP	0.98726	0.917
55DAP/53DAP	1.13085	0.656
57DAP/55DAP	1.0634	1
62DAP/57DAP	0.66091	0.028
68DAP/62DAP	0.87257	0.609
68DAP/14DAP	1.53819	0.558

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.91966	0.378

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.6351	0.17
Mature Green Tomato/Ripe Tomato	0.99268	0.715
Immature Eggplant/Mature Eggplant	6.25555	0.049
Ripe Pepper/Ripe Tomato	7.6877	0.256
Mature Eggplant/Ripe Tomato	1.63153	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.18626	0.591
1-1-2/M82	0.86053
12-2/M82	N/A	N/A
12-4/M82	0.99443
1-3/M82	0.76257	0.441
2-1-1/M82	0.74054	0.465
2-1/M82	N/A	N/A
2-6/M82	0.93363	1
3-2/M82	N/A	N/A
4-1-1/M82	0.8318	1
4-1/M82	1.16821
4-3-2/M82	1.00838	1
4-3/M82	0.95891
5-3/M82	1.06678	1
6-2/M82	0.66215
6-3/M82	N/A	N/A
7-1/M82	0.93138
7-2/M82	0.85086	0.527
9-3-2/M82	0.82474

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.53567	0.584
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.8494	0.418
IL12-4/WTpooled	0.99239	1
IL1-4/WTpooled	1.03601
WT/WTpooled	1.12248	0.785

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	0.9632	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02895	0.921
DC3000/delta hrp 6h	1.24508	1
DC3000/delta hrp 12h	1.01988	1
DC3000/delta hrp 24h	0.79819	0.049

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	0.47184	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.13612	0.254
Exp 36h	1.07976	1
Exp 60h	1.30073	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02275	1
Var 0h	1.22811	0.594
Var 12h I row2-row1	0.91885	0.77
Var 12h NI row2-row1	0.91391	0.713
Var 36h I row2-row1	1.07873	0.601
Var 36h NI row2-row1	1.08654	1
Var 60h I row2-row1	0.86873	0.832
Var 60h NI row2-row1	0.95684	0.932
Time course 0hI-0hNI	0.87219	0.129
Time course 12hI-12hNI	1.07491	0.73
Time course 36hI-36hNI	0.821	0.076
Time course 60hI-60hNI	0.74021	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)	1.00065	1
transgenic ySAMdc/azygous control (breaker)	0.79007	0.129
transgenic ySAMdc/azygous control (red)	0.98202	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.21055	0.036

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.53485	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.97229	0.172
Manapal/WT (break)	1.08028	1
Manapal/WT (red)	1.60511	0.15