Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.11.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1003	0.838
27DAP/17DAP	0.94252	0.911
39DAP/27DAP	0.91303	0.537
41DAP/39DAP	1.38065	0.289
42DAP/41DAP	0.98045	1
43DAP/42DAP	0.94584	0.877
47DAP/43DAP	0.84985	0.522
52DAP/47DAP	1.15572	0.69
57DAP/52DAP	1.02945	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92332	0.39
17DAP/reference	0.98201	0.819
27DAP/reference	1.03331	0.709
39DAP/reference	1.00734	0.871
41DAP/reference	0.98091	0.434
42DAP/reference	0.93562	0.052
43DAP/reference	1.01015	0.899
47DAP/reference	0.92546	0.007
52DAP/reference	0.84107	0.121
57DAP/reference	0.89064	0.071

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01174	0.923
27DAP/17DAP	1.02729	0.924
39DAP/27DAP	1.04302	0.677
41DAP/39DAP	0.99776	1
42DAP/41DAP	1.02577	0.893
43DAP/42DAP	1.05813	0.112
47DAP/43DAP	1.01805	0.914
52DAP/47DAP	0.92893	0.585
57DAP/52DAP	0.97022	0.646
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95103	0.129
17DAP/reference	0.96199	0.082
27DAP/reference	0.95537	0.101
39DAP/reference	1.00982	0.538
41DAP/reference	0.94021	0.086
42DAP/reference	0.92408	0.01
43DAP/reference	0.97418	0.334
47DAP/reference	0.94221	0.293
52DAP/reference	0.94073	0.196
57DAP/reference	0.96737	0.341

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95949	0.412
17DAP/reference	0.9527	0.337
27DAP/reference	0.97136	0.467
39DAP/reference	0.89214	0.091
41DAP/reference	0.89652	0.199
42DAP/reference	0.87856	0.021
43DAP/reference	0.91501	0.191
47DAP/reference	0.95644	0.284
52DAP/reference	0.91245	0.02
57DAP/reference	0.91442	0.278

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96387	0.087
17DAP/reference	0.96199	0.335
27DAP/reference	0.98025	0.376
39DAP/reference	0.96553	0.076
41DAP/reference	0.96437	0.237
42DAP/reference	0.90974	0.134
43DAP/reference	0.98254	0.545
47DAP/reference	0.97744	0.509
52DAP/reference	0.97508	0.582
57DAP/reference	0.76816	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04591	0.966
26DAP/20DAP	0.94671	1
34DAP/26DAP	0.95542	0.848
51DAP/34DAP	1.06351	0.637
52DAP/51DAP	1.01321	0.86
53DAP/52DAP	N/A	N/A
55DAP/53DAP	1.04175	0.79
57DAP/55DAP	1.02746	1
62DAP/57DAP	0.98331	0.994
68DAP/62DAP	1.34788	0.155
68DAP/14DAP	1.16833	0.541

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.89247	0.186

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.84719	0.058
Mature Green Tomato/Ripe Tomato	0.89092	0.377
Immature Eggplant/Mature Eggplant	1.57739	0.05
Ripe Pepper/Ripe Tomato	1.18794	1
Mature Eggplant/Ripe Tomato	0.4526	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.08061	0.742
1-1-2/M82	1.01026	1
12-2/M82	1.01091	1
12-4/M82	0.99806	1
1-3/M82	0.91287	0.378
2-1-1/M82	1.04913	0.764
2-1/M82	N/A	N/A
2-6/M82	0.94738	1
3-2/M82	0.89333	1
4-1-1/M82	0.98714	1
4-1/M82	1.07497	1
4-3-2/M82	0.85952	0.698
4-3/M82	1.05432	1
5-3/M82	0.99145	1
6-2/M82	0.96789	1
6-3/M82	0.94322	1
7-1/M82	0.96702
7-2/M82	1.02959	1
9-3-2/M82	0.8873	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.8464	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.19674	0.362
IL12-4/WTpooled	1.04531	0.785
IL1-4/WTpooled	1.02083	1
WT/WTpooled	1.04843	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	1.08968	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11035	0.692
DC3000/delta hrp 6h	0.9836	0.95
DC3000/delta hrp 12h	1.07873	1
DC3000/delta hrp 24h	1.04314	0.633

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.00831	0.648
DC3000 delta B/DC3000 delta AB	1.01118	0.714

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.21337	0.693
Exp 60h	1.25097	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98203	1
Var 0h	0.95915	1
Var 12h I row2-row1	1.09972	0.406
Var 12h NI row2-row1	1.04149	1
Var 36h I row2-row1	0.87864	1
Var 36h NI row2-row1	0.91171	0.478
Var 60h I row2-row1	1.17127	1
Var 60h NI row2-row1	1.11059	0.904
Time course 0hI-0hNI	1.03938	0.852
Time course 12hI-12hNI	1.03179	0.747
Time course 36hI-36hNI	1.05219	0.101
Time course 60hI-60hNI	1.11223	0.137

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)	1.00996	0.699
transgenic ySAMdc/azygous control (breaker)	0.90191	0.49
transgenic ySAMdc/azygous control (red)	1.0057	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00765	0.587

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.76269	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.81742	0.172
Manapal/WT (break)	1.00431	1
Manapal/WT (red)	0.79128	0.181