Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.10.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19733	0.932
27DAP/17DAP	0.9943	0.967
39DAP/27DAP	1.05665	0.899
41DAP/39DAP	0.88924	0.67
42DAP/41DAP	1.08284	0.903
43DAP/42DAP	0.81344	0.705
47DAP/43DAP	1.04234	0.876
52DAP/47DAP	1.56763	0.453
57DAP/52DAP	1.21961	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80115	0.038
17DAP/reference	0.9678	0.597
27DAP/reference	0.89144	0.295
39DAP/reference	1.01944	0.903
41DAP/reference	1.13795	0.48
42DAP/reference	0.73877	0.008
43DAP/reference	0.97665	0.763
47DAP/reference	0.78155	0.03
52DAP/reference	0.80751	0.128
57DAP/reference	0.98147	0.61

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87988	0.47
27DAP/17DAP	1.23529	0.328
39DAP/27DAP	0.99111	0.964
41DAP/39DAP	1.05542	1
42DAP/41DAP	0.94945	0.687
43DAP/42DAP	1.30247	0.23
47DAP/43DAP	1.21394	0.25
52DAP/47DAP	1.11187	0.666
57DAP/52DAP	0.92932	0.612
57DAP/7DAP	1.55217

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98769	0.682
17DAP/reference	0.86741	0.108
27DAP/reference	1.02978	0.301
39DAP/reference	0.97934	0.552
41DAP/reference	0.90031	0.247
42DAP/reference	0.99185	0.641
43DAP/reference	0.99741	0.694
47DAP/reference	0.8085	0.293
52DAP/reference	0.81626	0.061
57DAP/reference	0.88724	0.149

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06891	0.951
17DAP/reference	0.86542	0.159
27DAP/reference	0.86837	0.15
39DAP/reference	0.89442	0.306
41DAP/reference	0.96762	0.403
42DAP/reference	1.10639	1
43DAP/reference	1.22102	0.347
47DAP/reference	1.04789	0.867
52DAP/reference	0.8279	0.351
57DAP/reference	0.79321	0.278

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00822	0.699
17DAP/reference	0.90467	0.398
27DAP/reference	1.03836	0.871
39DAP/reference	0.82802	0.05
41DAP/reference	0.87739	0.293
42DAP/reference	0.86757	0.134
43DAP/reference	0.84856	0.237
47DAP/reference	0.99656	0.61
52DAP/reference	1.1578	0.674
57DAP/reference	0.77841	0.304

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.22031	0.966
26DAP/20DAP	1.56679	0.099
34DAP/26DAP	0.87146	0.702
51DAP/34DAP	0.95516	0.743
52DAP/51DAP	0.96082	1
53DAP/52DAP	0.58097	0.052
55DAP/53DAP	1.1188	0.991
57DAP/55DAP	1.44742	0.256
62DAP/57DAP	0.63985	0.088
68DAP/62DAP	0.94527	0.769
68DAP/14DAP	6.92424

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.83003	0.285

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.58829
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.00657
12-2/M82	0.69963
12-4/M82	1.0521
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	0.77753
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	2.11113
4-3/M82	N/A	N/A
5-3/M82	0.70607	0.447
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.87619
7-2/M82	1.22551
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.30261	0.277
IL2-6/WTpooled	0.58943	0.348
IL7-5/WTpooled	1.3581	0.67
IL7-3/WTpooled	1.39314	1
IL12-4/WTpooled	1.17698	0.557
IL1-4/WTpooled	0.67378	0.834
WT/WTpooled	1.02498	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	1.4561	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.16819	0.758
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.01549	1
DC3000/delta hrp 24h	1.32307	0.483

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	6.61919

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.11037	1
Exp 36h	N/A	N/A
Exp 60h	1.70057	0.226

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03668	1
Var 0h	0.72629	1
Var 12h I row2-row1	1.12052	0.544
Var 12h NI row2-row1	1.56059	1
Var 36h I row2-row1	1.24503	0.339
Var 36h NI row2-row1	0.63397	0.743
Var 60h I row2-row1	1.18753	0.543
Var 60h NI row2-row1	0.83714	0.313
Time course 0hI-0hNI	1.10834	0.662
Time course 12hI-12hNI	1.92204	0.019
Time course 36hI-36hNI	3.57275	0.005
Time course 60hI-60hNI	3.41578	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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	1.08096	1
transgenic ySAMdc/azygous control (red)	N/A	N/A

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99231	0.673

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.41861	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.86937	0.315