Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.8.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1437	0.561
27DAP/17DAP	1.08224	0.88
39DAP/27DAP	0.82952	0.447
41DAP/39DAP	1.2141	0.54
42DAP/41DAP	1.07535	0.908
43DAP/42DAP	0.94651	0.877
47DAP/43DAP	1.25656	0.481
52DAP/47DAP	1.20331	0.61
57DAP/52DAP	1.04978	0.993

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99517	0.743
17DAP/reference	1.09071	0.034
27DAP/reference	1.05064	0.569
39DAP/reference	1.01849	0.76
41DAP/reference	1.14708	0.025
42DAP/reference	0.95664	0.016
43DAP/reference	0.98414	0.728
47DAP/reference	1.00343	0.764
52DAP/reference	0.98449	0.564
57DAP/reference	1.01727	0.829

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8976	0.496
27DAP/17DAP	1.04077	0.969
39DAP/27DAP	1.0704	0.643
41DAP/39DAP	0.98162	0.997
42DAP/41DAP	1.07168	0.852
43DAP/42DAP	0.93499	0.482
47DAP/43DAP	1.02706	0.963
52DAP/47DAP	1.13896	0.593
57DAP/52DAP	1.01022	1
57DAP/7DAP	1.20746	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92905	0.296
17DAP/reference	1.04288	0.896
27DAP/reference	1.17701	0.014
39DAP/reference	1.2353	0.333
41DAP/reference	1.1484	0.363
42DAP/reference	1.16807	0.534
43DAP/reference	1.06244	0.802
47DAP/reference	1.1434	0.582
52DAP/reference	1.3445	0.028
57DAP/reference	1.14089	0.25

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9738	0.688
17DAP/reference	1.08052	0.063
27DAP/reference	1.03794	0.902
39DAP/reference	1.15443	0.247
41DAP/reference	0.91338	0.373
42DAP/reference	0.95146	0.392
43DAP/reference	1.00277	0.875
47DAP/reference	0.94011	0.253
52DAP/reference	1.11956	0.065
57DAP/reference	1.19273	0.06

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16914	0.366
17DAP/reference	0.89432	0.335
27DAP/reference	0.82765	0.27
39DAP/reference	1.06884	0.466
41DAP/reference	1.05378	0.674
42DAP/reference	0.69895	0.032
43DAP/reference	0.88485	0.092
47DAP/reference	0.94567	0.278
52DAP/reference	0.77228	0.184
57DAP/reference	0.74383	0.092

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98486	1
26DAP/20DAP	0.77662	0.244
34DAP/26DAP	0.9606	0.945
51DAP/34DAP	1.0109	0.883
52DAP/51DAP	1.09373	0.722
53DAP/52DAP	0.90555	0.776
55DAP/53DAP	1.529	0.234
57DAP/55DAP	1.04659	0.899
62DAP/57DAP	1.10652	0.833
68DAP/62DAP	0.87849	0.543
68DAP/14DAP	0.826

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.09046	0.591

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.03536	0.666
Mature Green Tomato/Ripe Tomato	0.99623	0.835
Immature Eggplant/Mature Eggplant	1.06685	0.321
Ripe Pepper/Ripe Tomato	2.11308	1
Mature Eggplant/Ripe Tomato	1.21301	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98032	0.944
1-1-2/M82	0.95401
12-2/M82	0.91995
12-4/M82	0.93777	1
1-3/M82	0.83793	0.376
2-1-1/M82	1.11983
2-1/M82	N/A	N/A
2-6/M82	1.07477	0.695
3-2/M82	0.87305
4-1-1/M82	0.84864	1
4-1/M82	1.00822
4-3-2/M82	0.9406	1
4-3/M82	0.75758	0.25
5-3/M82	0.95281	1
6-2/M82	0.8753
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.9384	0.881
9-3-2/M82	0.92702

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.15196	0.493
IL2-6/WTpooled	0.9228	1
IL7-5/WTpooled	0.81401
IL7-3/WTpooled	1.15299	1
IL12-4/WTpooled	0.83145	0.554
IL1-4/WTpooled	1.08991	1
WT/WTpooled	0.87975	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	1.003	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99403	1
DC3000/delta hrp 6h	1.07152	1
DC3000/delta hrp 12h	1.04422	1
DC3000/delta hrp 24h	1.05213	0.62

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.76008	0.413
DC3000 delta B/DC3000 delta AB	0.69519	0.023

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.30517	1
Exp 36h	0.93805	0.879
Exp 60h	0.90373	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97568	1
Var 0h	0.90862	1
Var 12h I row2-row1	0.86443	0.363
Var 12h NI row2-row1	0.94408	0.494
Var 36h I row2-row1	0.92629	0.805
Var 36h NI row2-row1	1.22525	1
Var 60h I row2-row1	1.50955	0.562
Var 60h NI row2-row1	1.01617	0.904
Time course 0hI-0hNI	1.02382	0.833
Time course 12hI-12hNI	0.96476	0.65
Time course 36hI-36hNI	0.90614	0.082
Time course 60hI-60hNI	0.55079	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)	0.9032	0.291
transgenic ySAMdc/azygous control (breaker)	0.95632	0.49
transgenic ySAMdc/azygous control (red)	0.97507	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97945	0.295

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.33631	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.90459	1
Manapal/WT (break)	0.87919	1
Manapal/WT (red)	1.21875	0.413