Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.12.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05248	0.893
27DAP/17DAP	1.56761	0.341
39DAP/27DAP	1.45134	0.229
41DAP/39DAP	0.84103	0.412
42DAP/41DAP	0.8682	1
43DAP/42DAP	1.0561	1
47DAP/43DAP	1.21053	0.415
52DAP/47DAP	0.938	0.8
57DAP/52DAP	0.82035	0.344

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97457	0.539
17DAP/reference	0.97122	0.208
27DAP/reference	1.09475	0.184
39DAP/reference	1.00018	1
41DAP/reference	0.96839	0.667
42DAP/reference	0.98184	0.398
43DAP/reference	0.98521	0.745
47DAP/reference	0.92902	0.083
52DAP/reference	0.97373	0.489
57DAP/reference	0.97775	0.435

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98982	0.801
27DAP/17DAP	0.97181	0.887
39DAP/27DAP	1.0109	1
41DAP/39DAP	0.98757	0.973
42DAP/41DAP	0.96956	0.752
43DAP/42DAP	0.95715	0.538
47DAP/43DAP	1.02573	0.884
52DAP/47DAP	0.98854	0.93
57DAP/52DAP	0.83197	0.082
57DAP/7DAP	1.13308	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.70011	0.032
17DAP/reference	1.69267	0.006
27DAP/reference	1.38455	0.011
39DAP/reference	1.11617	0.222
41DAP/reference	1.22243	0.032
42DAP/reference	1.34679	0.03
43DAP/reference	1.35392	0.034
47DAP/reference	1.14874	0.259
52DAP/reference	1.56777	0.008
57DAP/reference	1.43986	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92753	0.353
17DAP/reference	1.00723	0.898
27DAP/reference	0.99761	0.735
39DAP/reference	0.99043	0.586
41DAP/reference	1.01189	1
42DAP/reference	0.86348	0.05
43DAP/reference	0.96476	0.527
47DAP/reference	0.92683	0.048
52DAP/reference	1.10581	0.069
57DAP/reference	1.17376	0.094

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.25524	0.027
17DAP/reference	1.17703	0.362
27DAP/reference	1.35063	0.081
39DAP/reference	1.25351	0.018
41DAP/reference	1.32037	0.104
42DAP/reference	1.01132	1
43DAP/reference	0.98205	0.66
47DAP/reference	1.00087	0.731
52DAP/reference	1.27551	0.201
57DAP/reference	1.17842	0.204

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05294	0.966
26DAP/20DAP	1.12538	0.581
34DAP/26DAP	0.85906	0.286
51DAP/34DAP	0.79354	0.067
52DAP/51DAP	1.13151	0.439
53DAP/52DAP	0.95943	0.776
55DAP/53DAP	1.12586	0.737
57DAP/55DAP	1.07378	0.841
62DAP/57DAP	1.15008	0.257
68DAP/62DAP	0.82029	0.263
68DAP/14DAP	0.93259	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.3772	0.023

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.34472	0.113
Mature Green Tomato/Ripe Tomato	2.09275	0.017
Immature Eggplant/Mature Eggplant	1.21847	0.061
Ripe Pepper/Ripe Tomato	0.82602	0.293
Mature Eggplant/Ripe Tomato	0.76924	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95664	0.944
1-1-2/M82	0.96337	1
12-2/M82	1.12239	0.61
12-4/M82	0.9053	0.33
1-3/M82	0.99492	1
2-1-1/M82	0.98634	1
2-1/M82	0.85473
2-6/M82	0.91585	1
3-2/M82	0.85482
4-1-1/M82	0.79636	1
4-1/M82	1.02924
4-3-2/M82	N/A	N/A
4-3/M82	0.51876	0.578
5-3/M82	1.25988	1
6-2/M82	0.81661	0.481
6-3/M82	1.06358	1
7-1/M82	N/A	N/A
7-2/M82	1.12009	0.385
9-3-2/M82	0.59657	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.86254	0.383
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.32845	1
IL12-4/WTpooled	1.16589	0.553
IL1-4/WTpooled	0.90347	0.699
WT/WTpooled	0.93083	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	1.01434	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98842	1
DC3000/delta hrp 6h	1.04075	1
DC3000/delta hrp 12h	0.96112	1
DC3000/delta hrp 24h	1.18057	0.192

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.29028	0.05
DC3000 delta B/DC3000 delta AB	1.24755	0.196

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07707	1
Exp 36h	0.95263	0.879
Exp 60h	1.12298	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96821	1
Var 0h	0.84292	0.933
Var 12h I row2-row1	0.97762	0.565
Var 12h NI row2-row1	1.0124	1
Var 36h I row2-row1	1.05564	1
Var 36h NI row2-row1	1.05023	1
Var 60h I row2-row1	0.86744	0.439
Var 60h NI row2-row1	0.93931	1
Time course 0hI-0hNI	1.06273	0.764
Time course 12hI-12hNI	0.95374	0.716
Time course 36hI-36hNI	1.14258	0.19
Time course 60hI-60hNI	1.02289	0.673

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)	0.8217	0.246
transgenic ySAMdc/azygous control (breaker)	0.65791	0.251
transgenic ySAMdc/azygous control (red)	1.15068	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.12933	0.033

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.36896	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.36107	0.086
Manapal/WT (break)	0.88685	1
Manapal/WT (red)	1.00992	1