Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.9.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15465	0.646
27DAP/17DAP	0.89556	0.766
39DAP/27DAP	0.75563	0.449
41DAP/39DAP	1.73066	0.26
42DAP/41DAP	1.32155	0.938
43DAP/42DAP	1.02495	0.937
47DAP/43DAP	0.93714	0.699
52DAP/47DAP	1.43045	0.443
57DAP/52DAP	0.83732	0.827

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06117	0.179
17DAP/reference	1.04331	0.148
27DAP/reference	0.94803	0.369
39DAP/reference	1.02099	0.615
41DAP/reference	1.10003	0.054
42DAP/reference	0.9319	0.005
43DAP/reference	1.02143	0.617
47DAP/reference	0.90769	0.006
52DAP/reference	0.88298	0.053
57DAP/reference	0.81134	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9818	0.716
27DAP/17DAP	1.06641
39DAP/27DAP	1.05412	0.526
41DAP/39DAP	1.02948	0.817
42DAP/41DAP	0.95847	0.734
43DAP/42DAP	0.99453	0.991
47DAP/43DAP	0.97957	0.902
52DAP/47DAP	1.05069	0.851
57DAP/52DAP	0.99173	0.838
57DAP/7DAP	1.17212	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93797	0.224
17DAP/reference	0.94219	0.064
27DAP/reference	0.92625	0.048
39DAP/reference	0.91525	0.015
41DAP/reference	0.80352	0.039
42DAP/reference	0.71027	0.01
43DAP/reference	0.93849	0.22
47DAP/reference	0.93345	0.293
52DAP/reference	0.83408	0.09
57DAP/reference	0.89948	0.093

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09739	0.124
17DAP/reference	1.06279	0.448
27DAP/reference	0.93981	0.317
39DAP/reference	0.97026	0.469
41DAP/reference	0.92676	0.256
42DAP/reference	0.83801	0.039
43DAP/reference	1.09221	0.473
47DAP/reference	0.84047	0.01
52DAP/reference	1.01891	0.838
57DAP/reference	1.12779	0.244

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98021	0.489
17DAP/reference	1.01788	0.842
27DAP/reference	0.98199	0.286
39DAP/reference	0.9488	0.101
41DAP/reference	0.95365	0.07
42DAP/reference	0.94446	0.22
43DAP/reference	0.86446	0.179
47DAP/reference	0.93454	0.286
52DAP/reference	0.98623	0.747
57DAP/reference	0.64197	0.034

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00701	1
26DAP/20DAP	0.96618	1
34DAP/26DAP	1.00047	1
51DAP/34DAP	0.99229	0.924
52DAP/51DAP	1.02632	0.873
53DAP/52DAP	1.05138
55DAP/53DAP	0.98792	0.925
57DAP/55DAP	1.02715	1
62DAP/57DAP	1.17657	0.057
68DAP/62DAP	0.92721	0.641
68DAP/14DAP	0.95788	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.88103	0.358

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.55654	0.113
Mature Green Tomato/Ripe Tomato	0.9087	0.522
Immature Eggplant/Mature Eggplant	1.85241	0.05
Ripe Pepper/Ripe Tomato	1.41241	1
Mature Eggplant/Ripe Tomato	1.0024	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.91126	0.883
1-1-2/M82	0.91501	0.804
12-2/M82	1.199	1
12-4/M82	0.90086	1
1-3/M82	1.18612	1
2-1-1/M82	1.56636
2-1/M82	1.6743
2-6/M82	1.07756	1
3-2/M82	N/A	N/A
4-1-1/M82	0.95844	1
4-1/M82	1.05378	1
4-3-2/M82	0.88586	1
4-3/M82	1.03679
5-3/M82	0.97229	1
6-2/M82	0.93144	1
6-3/M82	0.96463	1
7-1/M82	1.0939
7-2/M82	1.05918	1
9-3-2/M82	0.80273	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.7491	0.321
IL2-6/WTpooled	0.79928	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.05374	0.362
IL12-4/WTpooled	0.70255	0.71
IL1-4/WTpooled	0.88546
WT/WTpooled	0.9441	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	0.81124	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95327	1
DC3000/delta hrp 6h	0.93952	0.95
DC3000/delta hrp 12h	1.16104	1
DC3000/delta hrp 24h	0.99427	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.09716	0.16
DC3000 delta B/DC3000 delta AB	1.04158	0.565

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98626	1
Exp 36h	1.06398	1
Exp 60h	1.18037	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0033	1
Var 0h	0.87549	0.933
Var 12h I row2-row1	1.09095	0.443
Var 12h NI row2-row1	0.9338	0.82
Var 36h I row2-row1	0.87032	0.575
Var 36h NI row2-row1	0.87528	0.549
Var 60h I row2-row1	1.19496	0.562
Var 60h NI row2-row1	1.24068	0.904
Time course 0hI-0hNI	1.08635	0.574
Time course 12hI-12hNI	1.04839	0.684
Time course 36hI-36hNI	0.9706	0.484
Time course 60hI-60hNI	1.35537	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)	0.94176	0.485
transgenic ySAMdc/azygous control (breaker)	1.10904	0.248
transgenic ySAMdc/azygous control (red)	1.08189	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99004	0.305

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.18868	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.07164	1
Manapal/WT (break)	0.76115	1
Manapal/WT (red)	0.75731	0.181