Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-6.4.6.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97734	0.823
27DAP/17DAP	0.7107	0.062
39DAP/27DAP	1.42267	0.229
41DAP/39DAP	1.12874	0.286
42DAP/41DAP	1.11732	0.941
43DAP/42DAP	1.24101	0.712
47DAP/43DAP	0.98904	0.902
52DAP/47DAP	0.93985	0.799
57DAP/52DAP	1.09985	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90821	0.3
17DAP/reference	1.09603	0.476
27DAP/reference	1.01784	0.831
39DAP/reference	1.07888	0.514
41DAP/reference	1.06046	0.714
42DAP/reference	0.93764	0.182
43DAP/reference	1.09074	0.382
47DAP/reference	0.91485	0.137
52DAP/reference	0.91255	0.131
57DAP/reference	1.02354	0.724

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.34523	0.086
27DAP/17DAP	1.11148	0.685
39DAP/27DAP	0.97303	0.852
41DAP/39DAP	0.99785	0.968
42DAP/41DAP	1.16635	0.478
43DAP/42DAP	1.24975	0.094
47DAP/43DAP	0.90171	0.332
52DAP/47DAP	0.86316	0.166
57DAP/52DAP	0.8101	0.258
57DAP/7DAP	1.09822	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05245	0.676
17DAP/reference	0.87949	0.253
27DAP/reference	0.89682	0.248
39DAP/reference	0.90756	0.307
41DAP/reference	1.20771	0.389
42DAP/reference	1.07521	0.889
43DAP/reference	1.15504	0.344
47DAP/reference	0.96848	0.671
52DAP/reference	0.90838	0.332
57DAP/reference	1.02509	0.775

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97991	0.756
17DAP/reference	1.04464	0.92
27DAP/reference	1.09061	0.66
39DAP/reference	0.80548	0.089
41DAP/reference	0.85595	0.098
42DAP/reference	1.08439	0.73
43DAP/reference	1.09671	0.885
47DAP/reference	1.22352	0.282
52DAP/reference	1.17552	0.061
57DAP/reference	1.03478	0.908

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.41976	0.18
17DAP/reference	1.02054	0.932
27DAP/reference	1.11068	0.672
39DAP/reference	0.95132	0.693
41DAP/reference	1.13949	0.383
42DAP/reference	1.11571	0.459
43DAP/reference	1.13406	0.755
47DAP/reference	0.98062	0.538
52DAP/reference	0.79509	0.211
57DAP/reference	1.13129	0.673

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05286	0.966
26DAP/20DAP	1.45562	0.361
34DAP/26DAP	0.87552	0.666
51DAP/34DAP	1.23696	0.909
52DAP/51DAP	0.94613	1
53DAP/52DAP	0.70593	0.164
55DAP/53DAP	0.86665	0.53
57DAP/55DAP	0.78757	0.151
62DAP/57DAP	0.61227	0.088
68DAP/62DAP	0.85719	0.747
68DAP/14DAP	0.99525	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	6.66665	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.06944	N/A
Mature Green Tomato/Ripe Tomato	1.02648	0.948
Immature Eggplant/Mature Eggplant	1.40229	0.05
Ripe Pepper/Ripe Tomato	4.5079	1
Mature Eggplant/Ripe Tomato	14.9077	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95244	0.944
1-1-2/M82	0.81799	N/A
12-2/M82	N/A	N/A
12-4/M82	0.93542	0.358
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	1.0814	0.967
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.94898	N/A
4-3/M82	0.8994	N/A
5-3/M82	1.00718	N/A
6-2/M82	1.04163	N/A
6-3/M82	1.21224	N/A
7-1/M82	0.68547	N/A
7-2/M82	0.91627	0.881
9-3-2/M82	0.98093	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.02257	N/A
IL2-6/WTpooled	1.18524	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.12682	0.362
IL12-4/WTpooled	1.20539	0.557
IL1-4/WTpooled	0.85695	0.415
WT/WTpooled	0.98278	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	1.09076	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07931	0.921
DC3000/delta hrp 6h	0.91206	0.95
DC3000/delta hrp 12h	1.15708	1
DC3000/delta hrp 24h	1.05663	0.728

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.66102	0.059
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.7505	0.328
Exp 36h	0.88799	0.749
Exp 60h	0.93966	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02592	1
Var 0h	0.87279	0.457
Var 12h I row2-row1	1.01132	1
Var 12h NI row2-row1	1.14434	0.649
Var 36h I row2-row1	1.13327	0.908
Var 36h NI row2-row1	1.34596	1
Var 60h I row2-row1	0.85707	0.832
Var 60h NI row2-row1	1.01761	1
Time course 0hI-0hNI	1.17797	0.262
Time course 12hI-12hNI	0.9569	0.637
Time course 36hI-36hNI	0.79611	0.023
Time course 60hI-60hNI	0.66055	0.006

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)	0.59592	0.299
transgenic ySAMdc/azygous control (breaker)	0.60023	0.137
transgenic ySAMdc/azygous control (red)	0.80377	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.21671	0.038

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.654	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.78841	0.172
Manapal/WT (break)	0.35631	0.285
Manapal/WT (red)	1.24864	1