Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.8.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81049	0.178
27DAP/17DAP	1.35879	0.73
39DAP/27DAP	1.59885	0.057
41DAP/39DAP	0.88822	0.543
42DAP/41DAP	1.24661	0.806
43DAP/42DAP	1.20011	0.867
47DAP/43DAP	0.66457	0.133
52DAP/47DAP	1.31213	0.645
57DAP/52DAP	1.12928	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.973	0.476
17DAP/reference	0.87744	0.298
27DAP/reference	1.11681	0.299
39DAP/reference	0.98085	0.75
41DAP/reference	0.91223	0.341
42DAP/reference	1.34498	0.009
43DAP/reference	1.01348	1
47DAP/reference	1.0421	1
52DAP/reference	1.13153	0.114
57DAP/reference	1.0731	0.682

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.74525	0.039
27DAP/17DAP	1.3786	0.154
39DAP/27DAP	0.803	0.075
41DAP/39DAP	1.11218	0.753
42DAP/41DAP	0.97779	0.764
43DAP/42DAP	1.12528	0.086
47DAP/43DAP	1.03504	0.822
52DAP/47DAP	0.89673	0.617
57DAP/52DAP	1.2997	0.148
57DAP/7DAP	1.10716	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95104	0.402
17DAP/reference	0.93931	0.338
27DAP/reference	1.16837	0.16
39DAP/reference	1.15629	0.538
41DAP/reference	1.18119	0.048
42DAP/reference	1.17416	0.233
43DAP/reference	1.0809	0.511
47DAP/reference	1.01159	1
52DAP/reference	1.30826	0.098
57DAP/reference	1.32126	0.031

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87005	0.342
17DAP/reference	0.89652	0.201
27DAP/reference	1.00415	0.686
39DAP/reference	0.94056	0.381
41DAP/reference	1.297	0.018
42DAP/reference	1.15305	0.259
43DAP/reference	1.15897	0.251
47DAP/reference	1.0932	0.353
52DAP/reference	0.99271	0.666
57DAP/reference	0.99844	0.834

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05806	0.809
17DAP/reference	0.91384	0.313
27DAP/reference	0.92125	0.302
39DAP/reference	0.87132	0.033
41DAP/reference	1.04224	0.826
42DAP/reference	0.95367	0.552
43DAP/reference	0.87117	0.294
47DAP/reference	1.21551	0.063
52DAP/reference	1.07806	1
57DAP/reference	1.15134	0.694

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.18219	0.966
26DAP/20DAP	1.8772	0.108
34DAP/26DAP	0.89268	0.874
51DAP/34DAP	1.13625	0.785
52DAP/51DAP	0.99806	1
53DAP/52DAP	1.21497	0.502
55DAP/53DAP	1.03596	0.955
57DAP/55DAP	1.10115	0.969
62DAP/57DAP	1.1256	0.8
68DAP/62DAP	0.85933	0.543
68DAP/14DAP	0.76783	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.92051	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	0.4355	0.026
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.08825	0.224
Mature Eggplant/Ripe Tomato	0.11989	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.66718	0.613
1-1-2/M82	1.43645	1
12-2/M82	1.28157	1
12-4/M82	0.72659	0.619
1-3/M82	1.90856	0.248
2-1-1/M82	0.67734	0.465
2-1/M82	0.82382	0.519
2-6/M82	0.72408	1
3-2/M82	0.63823
4-1-1/M82	0.85187	1
4-1/M82	N/A	N/A
4-3-2/M82	0.86858	1
4-3/M82	0.59963	0.578
5-3/M82	0.98955	1
6-2/M82	1.53306
6-3/M82	0.96932	1
7-1/M82	1.13239	0.925
7-2/M82	1.0505	1
9-3-2/M82	0.9199	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	5.54725	0.531
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.91643	1
IL12-4/WTpooled	1.03299	1
IL1-4/WTpooled	1.27026	0.364
WT/WTpooled	1.04315	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	1.13371	0.222

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.80118	1
DC3000/delta hrp 6h	0.86434	0.95
DC3000/delta hrp 12h	1.24023	1
DC3000/delta hrp 24h	0.86557	0.241

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.00768
DC3000 delta B/DC3000 delta AB	1.24209	0.212

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01522	1
Exp 36h	0.99787	0.943
Exp 60h	1.48661	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02951	1
Var 0h	1.09311	0.311
Var 12h I row2-row1	0.99181	1
Var 12h NI row2-row1	1.13228	0.34
Var 36h I row2-row1	1.17208	0.41
Var 36h NI row2-row1	0.8069	0.421
Var 60h I row2-row1	0.84293	0.293
Var 60h NI row2-row1	0.89392	0.483
Time course 0hI-0hNI	0.97672	0.908
Time course 12hI-12hNI	1.06778	0.493
Time course 36hI-36hNI	1.27872	0.007
Time course 60hI-60hNI	2.23773	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)	1.52157	0.384
transgenic ySAMdc/azygous control (breaker)	0.78659	0.251
transgenic ySAMdc/azygous control (red)	0.86118	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.62093	0.026

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.17787	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.96479	1
Manapal/WT (break)	0.86962	1
Manapal/WT (red)	0.82559	0.184