Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.10.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88571	0.436
27DAP/17DAP	1.1339	0.852
39DAP/27DAP	1.22597	0.572
41DAP/39DAP	0.73909	0.15
42DAP/41DAP	1.23545	0.73
43DAP/42DAP	1.56402	0.397
47DAP/43DAP	1.48616	0.187
52DAP/47DAP	0.89653	0.639
57DAP/52DAP	1.06443	0.987

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.4167	0.197
17DAP/reference	1.63078	0.034
27DAP/reference	1.06256	0.847
39DAP/reference	1.42258	0.045
41DAP/reference	1.77726	0.014
42DAP/reference	1.30013	0.053
43DAP/reference	1.28785	0.269
47DAP/reference	1.2904	0.207
52DAP/reference	1.05669	0.991
57DAP/reference	0.91282	0.221

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.29114	0.091
27DAP/17DAP	0.96779	0.887
39DAP/27DAP	1.02251	0.799
41DAP/39DAP	1.1406	0.807
42DAP/41DAP	1.18211	0.159
43DAP/42DAP	1.28569	0.027
47DAP/43DAP	0.99679	0.989
52DAP/47DAP	0.95473	0.814
57DAP/52DAP	1.14688	0.341
57DAP/7DAP	0.9321	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96168	0.445
17DAP/reference	0.87436	0.031
27DAP/reference	0.77045	0.01
39DAP/reference	0.85502	0.014
41DAP/reference	0.91103	0.116
42DAP/reference	0.87701	0.012
43DAP/reference	0.82826	0.061
47DAP/reference	1.13115	0.685
52DAP/reference	0.83035	0.014
57DAP/reference	0.87266	0.114

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13877	0.463
17DAP/reference	1.44508	0.02
27DAP/reference	1.33784	0.244
39DAP/reference	1.18888	0.239
41DAP/reference	1.17888	0.513
42DAP/reference	1.32209	0.03
43DAP/reference	1.23958	0.401
47DAP/reference	1.39319	0.024
52DAP/reference	1.37976	0.014
57DAP/reference	1.70204	0.038

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02436	1
17DAP/reference	1.06791	0.62
27DAP/reference	0.84034	0.078
39DAP/reference	0.86412	0.133
41DAP/reference	0.95497	0.459
42DAP/reference	0.8758	0.287
43DAP/reference	1.06312	1
47DAP/reference	1.87394	0.006
52DAP/reference	0.74115	0.18
57DAP/reference	1.07332	0.856

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.51418	0.005
26DAP/20DAP	1.34676	0.215
34DAP/26DAP	0.92892	0.879
51DAP/34DAP	1.1568	0.496
52DAP/51DAP	0.80619	1
53DAP/52DAP	1.11812	0.565
55DAP/53DAP	0.6403	0.037
57DAP/55DAP	1.48875	0.543
62DAP/57DAP	0.92393	0.871
68DAP/62DAP	0.79875	0.543
68DAP/14DAP	0.80646	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.62519	0.016

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.19379	0.666
Mature Green Tomato/Ripe Tomato	0.45296	0.055
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.56272	0.293
Mature Eggplant/Ripe Tomato	0.48896

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.47057
12-2/M82	N/A	N/A
12-4/M82	1.22604
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	1.23302	0.84
4-1-1/M82	N/A	N/A
4-1/M82	4.0747
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.85406
7-2/M82	N/A	N/A
9-3-2/M82	1.82387	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.75426
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.2334	0.362
IL12-4/WTpooled	1.19189	0.481
IL1-4/WTpooled	0.98105	0.834
WT/WTpooled	1.03455	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	1.05902	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91632	1
DC3000/delta hrp 6h	0.8435	0.95
DC3000/delta hrp 12h	1.2072	1
DC3000/delta hrp 24h	0.94018	0.629

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.80129	0.045
DC3000 delta B/DC3000 delta AB	0.90311	0.381

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.14539	1
Exp 36h	1.10583	1
Exp 60h	1.02034	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99602	1
Var 0h	0.90129	0.933
Var 12h I row2-row1	0.87746	0.363
Var 12h NI row2-row1	1.02356	1
Var 36h I row2-row1	1.24595	0.601
Var 36h NI row2-row1	0.98403	0.852
Var 60h I row2-row1	0.95681	0.582
Var 60h NI row2-row1	0.91435	0.866
Time course 0hI-0hNI	0.98012	0.94
Time course 12hI-12hNI	1.05008	0.678
Time course 36hI-36hNI	1.09273	0.248
Time course 60hI-60hNI	0.63773	0.007

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)	0.83134	0.314
transgenic ySAMdc/azygous control (breaker)	0.81198	0.173
transgenic ySAMdc/azygous control (red)	0.91681	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93511	0.115

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.04413	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.86023	1
Manapal/WT (break)	0.98227	1
Manapal/WT (red)	0.97412	0.863