Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.14.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17282	0.534
27DAP/17DAP	1.44641	0.532
39DAP/27DAP	1.29997	0.329
41DAP/39DAP	0.63978	0.066
42DAP/41DAP	1.02375	0.994
43DAP/42DAP	1.03031	1
47DAP/43DAP	1.08476	0.926
52DAP/47DAP	0.84691	0.598
57DAP/52DAP	1.15719	0.941

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.35402	0.071
17DAP/reference	1.36239	0.021
27DAP/reference	0.91871	0.349
39DAP/reference	1.24779	0.07
41DAP/reference	1.42627	0.023
42DAP/reference	1.35989	0.002
43DAP/reference	1.08816	0.471
47DAP/reference	1.23838	0.008
52DAP/reference	1.22305	0.388
57DAP/reference	0.96296	0.456

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15083	0.258
27DAP/17DAP	0.99507	0.969
39DAP/27DAP	0.98837	0.953
41DAP/39DAP	1.04448	0.807
42DAP/41DAP	0.98383	0.819
43DAP/42DAP	0.82014	0.058
47DAP/43DAP	1.04293	0.65
52DAP/47DAP	0.90566	0.572
57DAP/52DAP	0.87685	0.264
57DAP/7DAP	0.96227	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.58755	0.025
17DAP/reference	1.98204	0.007
27DAP/reference	1.63329	0.008
39DAP/reference	1.30595	0.013
41DAP/reference	1.61153	0.012
42DAP/reference	1.18665	0.014
43DAP/reference	1.32777	0.023
47DAP/reference	1.65265	0.014
52DAP/reference	1.55664	0.017
57DAP/reference	0.99299	0.569

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.33497	0.057
17DAP/reference	1.60408	0.008
27DAP/reference	1.27584	0.087
39DAP/reference	1.07529	0.514
41DAP/reference	1.45674	0.005
42DAP/reference	1.46016	0.01
43DAP/reference	1.44527	0.159
47DAP/reference	1.41075	0.009
52DAP/reference	1.44679	0.006
57DAP/reference	1.49662	0.055

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.03013	0.019
17DAP/reference	1.55845	0.217
27DAP/reference	1.52822	0.02
39DAP/reference	1.6302	0.005
41DAP/reference	1.1911	0.039
42DAP/reference	1.17709	0.258
43DAP/reference	1.4281	0.012
47DAP/reference	1.5045	0.022
52DAP/reference	1.42185	0.044
57DAP/reference	1.35418	0.01

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.87636	0.841
26DAP/20DAP	1.1395	0.77
34DAP/26DAP	0.99358	1
51DAP/34DAP	0.75215	0.078
52DAP/51DAP	0.95098	1
53DAP/52DAP	0.87168	0.35
55DAP/53DAP	1.12898	0.614
57DAP/55DAP	1.28126	0.559
62DAP/57DAP	1.05642	1
68DAP/62DAP	0.76886	0.406
68DAP/14DAP	0.65843	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.78389	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.90803	0.089
Mature Green Tomato/Ripe Tomato	1.88813	0.023
Immature Eggplant/Mature Eggplant	0.9046
Ripe Pepper/Ripe Tomato	0.62382
Mature Eggplant/Ripe Tomato	1.58555

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.2425
4-3-2/M82	1.32689	0.241
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	1.15376
7-2/M82	N/A	N/A
9-3-2/M82	1.0072	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.59789	0.277
IL2-6/WTpooled	1.20353	0.415
IL7-5/WTpooled	1.26524	1
IL7-3/WTpooled	0.94828	1
IL12-4/WTpooled	1.27904	0.673
IL1-4/WTpooled	1.17377	1
WT/WTpooled	1.00385	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	0.91037	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	0.97886	0.95
DC3000/delta hrp 12h	1.09229	1
DC3000/delta hrp 24h	0.83485	0.503

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.98549	0.961

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03743	1
Exp 36h	0.78246	0.589
Exp 60h	0.86267	0.32

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00516	1
Var 0h	0.75757	1
Var 12h I row2-row1	0.90923	0.565
Var 12h NI row2-row1	1.00864	1
Var 36h I row2-row1	1.15853	0.339
Var 36h NI row2-row1	1.12347	1
Var 60h I row2-row1	1.00947	1
Var 60h NI row2-row1	0.90494	0.818
Time course 0hI-0hNI	1.00947	1
Time course 12hI-12hNI	1.02796	0.811
Time course 36hI-36hNI	1.10966	0.035
Time course 60hI-60hNI	0.73258	0.015

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)	0.93417	0.362
transgenic ySAMdc/azygous control (breaker)	0.95781	0.49
transgenic ySAMdc/azygous control (red)	0.91229	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.892	0.431

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.07512	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.8628	0.105
Manapal/WT (break)	2.36804	0.123
Manapal/WT (red)	0.43018	1