Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-1.4.9.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.30632	0.381
27DAP/17DAP	0.83129	0.585
39DAP/27DAP	0.84232	0.487
41DAP/39DAP	1.21668	0.28
42DAP/41DAP	1.06471	0.937
43DAP/42DAP	1.04511	1
47DAP/43DAP	1.30855	0.442
52DAP/47DAP	1.00669	0.9
57DAP/52DAP	1.13588	0.837

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04451	0.5
17DAP/reference	1.03078	0.342
27DAP/reference	1.03415	0.478
39DAP/reference	1.09205	0.089
41DAP/reference	1.01763	0.814
42DAP/reference	1.174	0.002
43DAP/reference	0.98136	0.594
47DAP/reference	1.09396	0.015
52DAP/reference	1.08832	0.038
57DAP/reference	1.12878	0.073

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01953	0.91
27DAP/17DAP	1.00727	0.988
39DAP/27DAP	0.99927	1
41DAP/39DAP	1.12562	0.224
42DAP/41DAP	0.98943	0.864
43DAP/42DAP	0.94929	0.321
47DAP/43DAP	1.01308	0.906
52DAP/47DAP	0.9452	0.801
57DAP/52DAP	1.0229	0.891
57DAP/7DAP	0.94479	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9135	0.129
17DAP/reference	0.93972	0.049
27DAP/reference	1.0175	0.197
39DAP/reference	0.98033	0.146
41DAP/reference	0.91156	0.029
42DAP/reference	0.86411	0.01
43DAP/reference	0.9289	0.082
47DAP/reference	0.96555	0.383
52DAP/reference	0.91413	0.163
57DAP/reference	0.90668	0.069

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14781	0.162
17DAP/reference	1.0968	0.32
27DAP/reference	0.92226	0.366
39DAP/reference	1.04885	0.556
41DAP/reference	1.2035	0.394
42DAP/reference	0.94813	0.433
43DAP/reference	1.04365	0.793
47DAP/reference	1.01206	0.751
52DAP/reference	1.16089	0.027
57DAP/reference	1.13157	0.286

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99132	0.699
17DAP/reference	0.9579	0.348
27DAP/reference	0.98165	0.539
39DAP/reference	0.99197	0.643
41DAP/reference	0.93459	0.055
42DAP/reference	0.95103	0.361
43DAP/reference	0.97729	0.484
47DAP/reference	0.96431	0.371
52DAP/reference	1.03926	0.779
57DAP/reference	0.89031	0.293

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02662	0.966
26DAP/20DAP	0.99023	1
34DAP/26DAP	1.02802	1
51DAP/34DAP	1.061	0.473
52DAP/51DAP	0.98992	1
53DAP/52DAP	N/A	N/A
55DAP/53DAP	0.95503	N/A
57DAP/55DAP	1.00747	0.953
62DAP/57DAP	1.02977	0.833
68DAP/62DAP	1.07807	0.8
68DAP/14DAP	1.01985	0.802

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02604	0.496

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.4053	N/A
Mature Green Tomato/Ripe Tomato	0.93871	0.569
Immature Eggplant/Mature Eggplant	1.3145	0.136
Ripe Pepper/Ripe Tomato	0.31735	0.224
Mature Eggplant/Ripe Tomato	0.43017	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.13414	N/A
1-1-2/M82	N/A	N/A
12-2/M82	0.91514	N/A
12-4/M82	1.03661	N/A
1-3/M82	1.17813	1
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.97758	N/A
3-2/M82	N/A	N/A
4-1-1/M82	0.84526	1
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.77157	0.326
5-3/M82	1.04732	1
6-2/M82	0.92636	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.91913	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.86722	0.383
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.99869	1
IL12-4/WTpooled	1.20017	0.557
IL1-4/WTpooled	0.96866	N/A
WT/WTpooled	0.98948	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	0.96106	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00291	1
DC3000/delta hrp 6h	1.16816	1
DC3000/delta hrp 12h	0.95891	1
DC3000/delta hrp 24h	1.04648	0.673

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.06492	0.094
DC3000 delta B/DC3000 delta AB	1.13494	0.284

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.16599	1
Exp 36h	1.18178	0.693
Exp 60h	1.34286	0.226

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96713	1
Var 0h	1.08245	1
Var 12h I row2-row1	1.21161	0.19
Var 12h NI row2-row1	1.0228	1
Var 36h I row2-row1	0.9707	1
Var 36h NI row2-row1	0.96035	0.549
Var 60h I row2-row1	1.1215	1
Var 60h NI row2-row1	1.15014	0.904
Time course 0hI-0hNI	1.05421	0.867
Time course 12hI-12hNI	1.04564	0.803
Time course 36hI-36hNI	1.04651	0.799
Time course 60hI-60hNI	2.82925	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)	0.91058	0.324
transgenic ySAMdc/azygous control (breaker)	0.91967	0.251
transgenic ySAMdc/azygous control (red)	1.00419	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98052	0.066

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88396	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.60169	0.09
Manapal/WT (break)	1.38466	0.13
Manapal/WT (red)	1.44689	0.15