Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.10.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1575	0.588
27DAP/17DAP	1.02714	1
39DAP/27DAP	0.65199	0.421
41DAP/39DAP	1.35415	0.63
42DAP/41DAP	1.12257	0.886
43DAP/42DAP	0.94124	0.887
47DAP/43DAP	1.23395	0.702
52DAP/47DAP	0.89687	0.694
57DAP/52DAP	1.06455	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89211	0.167
17DAP/reference	0.90745	0.169
27DAP/reference	0.94708	0.249
39DAP/reference	1.0142	0.786
41DAP/reference	0.90813	0.114
42DAP/reference	0.90026	0.04
43DAP/reference	1.03709	0.678
47DAP/reference	1.03352	0.685
52DAP/reference	1.16211	0.059
57DAP/reference	1.37662	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9728	0.763
27DAP/17DAP	0.99025	0.943
39DAP/27DAP	1.04155	0.707
41DAP/39DAP	1.24704	0.012
42DAP/41DAP	0.89706	0.335
43DAP/42DAP	0.76812	0.027
47DAP/43DAP	1.104	0.65
52DAP/47DAP	0.90097	0.546
57DAP/52DAP	0.88581	0.484
57DAP/7DAP	0.9119	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92206	0.129
17DAP/reference	0.94858	0.22
27DAP/reference	0.97485	0.43
39DAP/reference	0.92131	0.126
41DAP/reference	0.93692	0.127
42DAP/reference	0.79198	0.01
43DAP/reference	0.74633	0.02
47DAP/reference	0.94442	0.504
52DAP/reference	0.70436	0.012
57DAP/reference	0.70987	0.024

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95558	0.58
17DAP/reference	0.94768	0.337
27DAP/reference	1.24437	0.041
39DAP/reference	1.02348	1
41DAP/reference	0.94958	0.364
42DAP/reference	0.91366	0.046
43DAP/reference	1.17272	0.05
47DAP/reference	0.84363	0.24
52DAP/reference	1.01012	1
57DAP/reference	0.90272	0.156

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05276	0.793
17DAP/reference	0.91937	0.255
27DAP/reference	0.929	0.243
39DAP/reference	0.96921	0.504
41DAP/reference	0.99867	0.826
42DAP/reference	1.05992	0.612
43DAP/reference	0.98423	0.66
47DAP/reference	0.90615	0.224
52DAP/reference	1.03518	0.979
57DAP/reference	1.14739	0.255

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01341	1
26DAP/20DAP	0.53276	0.512
34DAP/26DAP	2.16998
51DAP/34DAP	0.76175	0.252
52DAP/51DAP	1.48836	0.606
53DAP/52DAP	0.87092	0.677
55DAP/53DAP	1.06679	0.826
57DAP/55DAP	1.44257	0.067
62DAP/57DAP	0.83326	0.681
68DAP/62DAP	1.47651	0.057
68DAP/14DAP	0.88218

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.05095	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	2.24374	0.02
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.08437	1
Mature Eggplant/Ripe Tomato	0.21108	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09557	0.536
1-1-2/M82	1.00681	1
12-2/M82	1.00997	1
12-4/M82	0.9919	1
1-3/M82	0.97104	0.441
2-1-1/M82	1.01241
2-1/M82	N/A	N/A
2-6/M82	1.24113	0.594
3-2/M82	1.07549
4-1-1/M82	2.15599
4-1/M82	1.09084
4-3-2/M82	1.44139
4-3/M82	1.84527	0.268
5-3/M82	1.00617	0.467
6-2/M82	1.19051
6-3/M82	0.72376
7-1/M82	N/A	N/A
7-2/M82	0.93399
9-3-2/M82	1.40088	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.07493	1
IL2-6/WTpooled	0.95096	1
IL7-5/WTpooled	1.11535	1
IL7-3/WTpooled	0.85583	1
IL12-4/WTpooled	1.00957	1
IL1-4/WTpooled	0.93285	0.562
WT/WTpooled	1.00401	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	0.88218	0.209

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01826	0.921
DC3000/delta hrp 6h	1.03507	0.95
DC3000/delta hrp 12h	1.1031	1
DC3000/delta hrp 24h	1.15562	0.383

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.15639	0.313
DC3000 delta B/DC3000 delta AB	1.28281	0.332

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89036	1
Exp 36h	0.93974	0.879
Exp 60h	0.87929	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97515	1
Var 0h	0.78534	0.933
Var 12h I row2-row1	0.9543	0.77
Var 12h NI row2-row1	1.0735	1
Var 36h I row2-row1	1.09055	0.309
Var 36h NI row2-row1	1.07457	1
Var 60h I row2-row1	0.86286	0.374
Var 60h NI row2-row1	0.92629	0.977
Time course 0hI-0hNI	1.02055	1
Time course 12hI-12hNI	1.05412	0.747
Time course 36hI-36hNI	1.10987	0.166
Time course 60hI-60hNI	1.04654	0.426

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)	0.95704	0.485
transgenic ySAMdc/azygous control (breaker)	0.74995	0.142
transgenic ySAMdc/azygous control (red)	1.15289	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98473	0.431

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.43326	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.96904	1
Manapal/WT (break)	1.50805	0.13
Manapal/WT (red)	1.36983	0.222