Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.6.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89774	0.464
27DAP/17DAP	1.21849	0.822
39DAP/27DAP	0.97198	0.719
41DAP/39DAP	1.05125	0.978
42DAP/41DAP	1.26902	0.647
43DAP/42DAP	1.10679	0.94
47DAP/43DAP	1.25095	0.474
52DAP/47DAP	0.83445	0.538
57DAP/52DAP	1.1502	0.941

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01453	0.814
17DAP/reference	1.03798	0.27
27DAP/reference	0.95848	0.406
39DAP/reference	1.04128	0.262
41DAP/reference	1.01939	0.312
42DAP/reference	0.95088	0.196
43DAP/reference	1.02312	0.646
47DAP/reference	0.89902	0.065
52DAP/reference	0.89063	0.028
57DAP/reference	0.83967	0.016

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98889	0.782
27DAP/17DAP	1.05777	0.831
39DAP/27DAP	0.91726	0.405
41DAP/39DAP	1.06242	0.79
42DAP/41DAP	1.10969	0.727
43DAP/42DAP	0.98409	0.854
47DAP/43DAP	1.0547	0.873
52DAP/47DAP	1.03379	0.907
57DAP/52DAP	0.88482	0.428
57DAP/7DAP	0.93641	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.46304	0.045
17DAP/reference	1.12182	1
27DAP/reference	0.85126	0.248
39DAP/reference	0.94565	0.354
41DAP/reference	0.90359	0.02
42DAP/reference	1.28188	0.686
43DAP/reference	0.9572	0.459
47DAP/reference	1.03602	0.854
52DAP/reference	1.53165	0.02
57DAP/reference	0.99209	0.513

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02061	0.823
17DAP/reference	1.06805	0.216
27DAP/reference	0.94744	0.34
39DAP/reference	1.00983	1
41DAP/reference	0.89085	0.06
42DAP/reference	0.88134	0.073
43DAP/reference	1.0064	0.736
47DAP/reference	0.86593	0.015
52DAP/reference	1.04756	0.368
57DAP/reference	1.03656	0.916

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.72128	0.119
17DAP/reference	0.97458	0.739
27DAP/reference	1.08555
39DAP/reference	0.83887	0.299
41DAP/reference	1.06645	1
42DAP/reference	0.99875	0.671
43DAP/reference	1.07565	1
47DAP/reference	0.93064	0.207
52DAP/reference	1.14606	0.601
57DAP/reference	0.55938	0.019

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05536	0.966
26DAP/20DAP	1.04453	1
34DAP/26DAP	0.96877	0.954
51DAP/34DAP	1.19402	0.387
52DAP/51DAP	1.07591	0.638
53DAP/52DAP	1.02751	0.944
55DAP/53DAP	1.10406	0.452
57DAP/55DAP	0.99562	0.923
62DAP/57DAP	1.15496	0.515
68DAP/62DAP	0.97513	0.834
68DAP/14DAP	1.0572	0.802

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.07352	0.627

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.80338	0.371
Mature Green Tomato/Ripe Tomato	1.07076	1
Immature Eggplant/Mature Eggplant	1.12051	0.123
Ripe Pepper/Ripe Tomato	0.7811	1
Mature Eggplant/Ripe Tomato	1.17473	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.86268
1-1-2/M82	1.1291
12-2/M82	0.94824
12-4/M82	0.92821	0.619
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	1.03052
2-6/M82	1.14617	0.505
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.04669	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.91683
9-3-2/M82	0.82759

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.10846	0.365
IL2-6/WTpooled	1.02018	0.788
IL7-5/WTpooled	1.17043	0.792
IL7-3/WTpooled	1.13771	0.362
IL12-4/WTpooled	0.85662	0.71
IL1-4/WTpooled	1.07561	1
WT/WTpooled	0.94034	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	1.33605	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99067	1
DC3000/delta hrp 6h	0.84318	0.95
DC3000/delta hrp 12h	1.20011	1
DC3000/delta hrp 24h	1.08542	0.174

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	0.68618	0.103

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.20341	1
Exp 60h	1.28136	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.69703	1
Var 0h	1.11396	0.594
Var 12h I row2-row1	1.0736	0.544
Var 12h NI row2-row1	0.89702	0.713
Var 36h I row2-row1	0.96841	1
Var 36h NI row2-row1	0.8534	1
Var 60h I row2-row1	0.99287	0.582
Var 60h NI row2-row1	1.05952	0.904
Time course 0hI-0hNI	0.99126	1
Time course 12hI-12hNI	1.02663	0.788
Time course 36hI-36hNI	1.06398	0.316
Time course 60hI-60hNI	1.23598	0.022

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)	1.08256	0.312
transgenic ySAMdc/azygous control (breaker)	1.03261	1
transgenic ySAMdc/azygous control (red)	0.93946	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02511	0.287

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.10518	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.90378	1
Manapal/WT (break)	0.89856	1
Manapal/WT (red)	1.02812	1