Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.17.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91344	0.551
27DAP/17DAP	0.89897	0.766
39DAP/27DAP	1.52067	0.192
41DAP/39DAP	0.84456	0.424
42DAP/41DAP	0.87758	1
43DAP/42DAP	1.21491	0.962
47DAP/43DAP	0.8188	0.433
52DAP/47DAP	1.34056	0.453
57DAP/52DAP	1.16852	0.859

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18518	0.441
17DAP/reference	1.01724	0.874
27DAP/reference	1.2507	0.026
39DAP/reference	1.07562	0.706
41DAP/reference	1.359	0.014
42DAP/reference	1.43276	0.001
43DAP/reference	1.03126	0.866
47DAP/reference	1.41032	0.008
52DAP/reference	1.36486	0.217
57DAP/reference	1.31839	0.047

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.29258	0.284
27DAP/17DAP	1.22023	0.604
39DAP/27DAP	0.98904	0.898
41DAP/39DAP	1.12733	0.735
42DAP/41DAP	1.01477	0.887
43DAP/42DAP	0.85307	0.143
47DAP/43DAP	1.14781	0.448
52DAP/47DAP	0.96747	0.886
57DAP/52DAP	1.26456	0.146
57DAP/7DAP	1.22572	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20482	0.173
17DAP/reference	1.0159	1
27DAP/reference	1.22225	0.015
39DAP/reference	0.91658	0.307
41DAP/reference	1.13352	0.416
42DAP/reference	0.86945	0.073
43DAP/reference	0.92755	0.23
47DAP/reference	1.34527	0.133
52DAP/reference	0.86085	0.115
57DAP/reference	0.92787	0.28

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99786	0.884
17DAP/reference	1.42181	0.367
27DAP/reference	1.34553	0.02
39DAP/reference	1.09901	0.912
41DAP/reference	1.33701	0.035
42DAP/reference	1.26519	0.081
43DAP/reference	1.34742	0.144
47DAP/reference	1.17515	0.052
52DAP/reference	1.28348	0.417
57DAP/reference	1.03604	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17945	0.142
17DAP/reference	0.9247	0.47
27DAP/reference	1.02834	0.621
39DAP/reference	1.03543	0.987
41DAP/reference	1.00102	0.754
42DAP/reference	1.08501	0.979
43DAP/reference	1.34512	0.302
47DAP/reference	1.43425	0.207
52DAP/reference	0.72695	0.098
57DAP/reference	1.0972	0.592

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.3639	0.817
26DAP/20DAP	1.74853	0.099
34DAP/26DAP	0.98755	0.988
51DAP/34DAP	1.8871	0.032
52DAP/51DAP	0.69635	0.151
53DAP/52DAP	2.24941	0.02
55DAP/53DAP	0.75103	0.044
57DAP/55DAP	0.87736	0.548
62DAP/57DAP	0.69083	0.028
68DAP/62DAP	1.43594	0.305
68DAP/14DAP	4.3727	0.436

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.53525	0.022

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.50801
Mature Green Tomato/Ripe Tomato	1.35251	0.086
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	2.55259
Mature Eggplant/Ripe Tomato	2.409	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.62524
1-1-2/M82	0.84865
12-2/M82	N/A	N/A
12-4/M82	0.83987	0.619
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	1.03606
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.84724
4-3/M82	0.7727
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	1.67797
7-1/M82	0.9119	0.803
7-2/M82	0.88883
9-3-2/M82	0.87467	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.95076	1
IL7-5/WTpooled	0.56937
IL7-3/WTpooled	0.95742	1
IL12-4/WTpooled	1.19393	0.595
IL1-4/WTpooled	1.11219	1
WT/WTpooled	0.97874	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	0.96606	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.88869	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	1.04457	0.76

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.3097	0.046
DC3000 delta B/DC3000 delta AB	1.17534	0.261

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

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

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

hybridization	ratio	FDR (corrected p value)
self-self	1.18028	1
Var 0h	1.7344	0.98
Var 12h I row2-row1	1.04469	0.795
Var 12h NI row2-row1	1.26343	0.34
Var 36h I row2-row1	1.16622	0.309
Var 36h NI row2-row1	0.8989	0.645
Var 60h I row2-row1	0.82055	0.374
Var 60h NI row2-row1	0.89571	0.818
Time course 0hI-0hNI	0.99874	1
Time course 12hI-12hNI	1.06937	0.678
Time course 36hI-36hNI	1.25274	0.07
Time course 60hI-60hNI	1.51289	0.009

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)	N/A	N/A
transgenic ySAMdc/azygous control (red)	1.30321	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.30788	0.237

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)	1.72784	0.126
Manapal/WT (red)	0.93187	0.424