Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.15.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00245	0.919
27DAP/17DAP	1.17769	0.845
39DAP/27DAP	0.72997	0.326
41DAP/39DAP	1.23503	0.619
42DAP/41DAP	1.01157	1
43DAP/42DAP	0.93569	0.877
47DAP/43DAP	1.08817	0.609
52DAP/47DAP	0.88465	0.673
57DAP/52DAP	0.83732	0.678

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31626	0.055
17DAP/reference	1.13986	0.154
27DAP/reference	1.13159	0.258
39DAP/reference	1.13743	0.209
41DAP/reference	1.2047	0.024
42DAP/reference	0.94597	0.211
43DAP/reference	0.9804	0.708
47DAP/reference	1.01033	1
52DAP/reference	0.91038	0.195
57DAP/reference	0.75821	0.112

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.61355	0.068
27DAP/17DAP	0.94541	0.878
39DAP/27DAP	1.22971	0.441
41DAP/39DAP	0.89947	0.586
42DAP/41DAP	1.01092	1
43DAP/42DAP	1.01551	0.746
47DAP/43DAP	1.12095	0.765
52DAP/47DAP	1.22912	0.463
57DAP/52DAP	0.88303	0.322
57DAP/7DAP	0.95766	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9062	0.08
17DAP/reference	0.89807	0.031
27DAP/reference	0.85246	0.01
39DAP/reference	0.93489	0.056
41DAP/reference	0.98544	0.449
42DAP/reference	0.96195	0.13
43DAP/reference	0.87099	0.011
47DAP/reference	1.00007	1
52DAP/reference	0.8701	0.014
57DAP/reference	0.86244	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13251	0.151
17DAP/reference	1.42238	0.12
27DAP/reference	1.27811	0.046
39DAP/reference	1.33793	0.112
41DAP/reference	1.17197	0.48
42DAP/reference	1.17799	0.176
43DAP/reference	1.43016	0.157
47DAP/reference	1.16117	0.063
52DAP/reference	1.41359	0.3
57DAP/reference	1.14729	0.306

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84501	0.038
17DAP/reference	1.17893	0.612
27DAP/reference	0.86898	0.025
39DAP/reference	0.9573	0.43
41DAP/reference	1.02723	1
42DAP/reference	1.08561	0.907
43DAP/reference	0.98813	0.639
47DAP/reference	1.00626	0.593
52DAP/reference	0.86564	0.167
57DAP/reference	1.41388	0.083

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07159	1
26DAP/20DAP	0.73971	0.512
34DAP/26DAP	1.26818	0.542
51DAP/34DAP	1.04309	0.883
52DAP/51DAP	0.90252
53DAP/52DAP	1.2821	0.398
55DAP/53DAP	1.08467	0.982
57DAP/55DAP	1.20551	0.525
62DAP/57DAP	0.87424	0.681
68DAP/62DAP	1.334	0.864
68DAP/14DAP	1.0471	0.958

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.52071	0.466

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.83427	0.058
Mature Green Tomato/Ripe Tomato	0.87497	0.569
Immature Eggplant/Mature Eggplant	0.67641	0.134
Ripe Pepper/Ripe Tomato	0.46291	0.224
Mature Eggplant/Ripe Tomato	0.88961	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00233	1
1-1-2/M82	1.11528	0.977
12-2/M82	1.08801	1
12-4/M82	0.905	1
1-3/M82	N/A	N/A
2-1-1/M82	1.02712	1
2-1/M82	N/A	N/A
2-6/M82	1.10391	0.695
3-2/M82	1.058
4-1-1/M82	0.92298	1
4-1/M82	0.83742	1
4-3-2/M82	0.84581	0.698
4-3/M82	1.019	1
5-3/M82	1.04485	1
6-2/M82	1.59957
6-3/M82	1.01197	1
7-1/M82	1.3459
7-2/M82	0.98664	1
9-3-2/M82	0.83283	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.10748	0.415
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.80844	0.418
IL12-4/WTpooled	1.15735	0.839
IL1-4/WTpooled	1.18843	1
WT/WTpooled	1.10829	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	0.7324	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0201	0.921
DC3000/delta hrp 6h	1.51815	1
DC3000/delta hrp 12h	1.02993	1
DC3000/delta hrp 24h	1.01839	0.728

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.89754	0.388
DC3000 delta B/DC3000 delta AB	0.98305	0.936

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.26168	1
Exp 36h	0.74298	0.321
Exp 60h	0.83431	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00302
Var 0h	0.78125	0.933
Var 12h I row2-row1	0.99742	1
Var 12h NI row2-row1	0.93145	0.713
Var 36h I row2-row1	0.94673	1
Var 36h NI row2-row1	0.84008	0.469
Var 60h I row2-row1	0.99773	0.952
Var 60h NI row2-row1	1.05626	0.904
Time course 0hI-0hNI	0.92954	0.458
Time course 12hI-12hNI	1.0532	0.633
Time course 36hI-36hNI	0.90068	0.183
Time course 60hI-60hNI	0.7573	0.011

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)	1.00872	0.921
transgenic ySAMdc/azygous control (breaker)	0.63111	0.118
transgenic ySAMdc/azygous control (red)	0.88739	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96855	0.231

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.71872	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.42949	0.088
Manapal/WT (break)	1.57852	0.183
Manapal/WT (red)	1.19214	0.222