Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.9.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05733	0.893
27DAP/17DAP	0.71059	0.147
39DAP/27DAP	1.2284	0.575
41DAP/39DAP	1.21347	0.676
42DAP/41DAP	2.18988	0.023
43DAP/42DAP	0.90497	0.799
47DAP/43DAP	1.1363	0.668
52DAP/47DAP	0.82634	0.539
57DAP/52DAP	1.02854	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.79796	0.007
17DAP/reference	1.40341	0.049
27DAP/reference	1.07711	0.264
39DAP/reference	1.38097	0.046
41DAP/reference	1.34323	0.016
42DAP/reference	1.80192	0.001
43DAP/reference	1.20151	0.044
47DAP/reference	1.14788	0.329
52DAP/reference	0.6558	0.018
57DAP/reference	0.7968	0.036

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00942	1
27DAP/17DAP	1.06227	0.751
39DAP/27DAP	1.06411	0.643
41DAP/39DAP	1.01805	0.849
42DAP/41DAP	0.94887	0.529
43DAP/42DAP	1.07054	0.297
47DAP/43DAP	1.00506	0.973
52DAP/47DAP	0.99779	0.97
57DAP/52DAP	0.96703	0.651
57DAP/7DAP	1.25556	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.44076	0.026
17DAP/reference	1.05867	0.328
27DAP/reference	1.10852	0.014
39DAP/reference	1.26017	0.007
41DAP/reference	1.25165	0.017
42DAP/reference	1.2417	0.037
43DAP/reference	1.05525	0.672
47DAP/reference	1.76126	0.032
52DAP/reference	1.36751	0.017
57DAP/reference	1.18976	0.087

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19892	0.3
17DAP/reference	2.24954	0.009
27DAP/reference	1.85529	0.021
39DAP/reference	1.56434	0.056
41DAP/reference	1.44282	0.188
42DAP/reference	1.86653	0.007
43DAP/reference	1.28316	0.575
47DAP/reference	2.04108	0.008
52DAP/reference	1.19075	0.135
57DAP/reference	1.41057	0.437

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.25934	0.045
17DAP/reference	1.22377	0.365
27DAP/reference	0.97295	0.539
39DAP/reference	1.08497	0.169
41DAP/reference	0.979	0.56
42DAP/reference	1.29904	0.307
43DAP/reference	1.50269	0.092
47DAP/reference	1.24905	0.355
52DAP/reference	1.00666	1
57DAP/reference	0.91208	0.299

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	2.61548	1
26DAP/20DAP	1.10294	0.598
34DAP/26DAP	1.08271	1
51DAP/34DAP	0.86793	0.155
52DAP/51DAP	1.09698	0.51
53DAP/52DAP	0.99361	0.978
55DAP/53DAP	1.04892	0.813
57DAP/55DAP	0.92104	0.67
62DAP/57DAP	0.99129	0.994
68DAP/62DAP	1.05829	0.956
68DAP/14DAP	0.4596	0.09

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.82681	0.022

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.95149	0.648
Mature Green Tomato/Ripe Tomato	0.59059	0.025
Immature Eggplant/Mature Eggplant	1.72373	0.05
Ripe Pepper/Ripe Tomato	1.00769	1
Mature Eggplant/Ripe Tomato	1.22828	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.76386
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	N/A	N/A
4-3-2/M82	1.345
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	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	2.02771

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.16713	0.277
IL2-6/WTpooled	1.08591	0.419
IL7-5/WTpooled	0.97099	1
IL7-3/WTpooled	1.09651	1
IL12-4/WTpooled	1.0201	0.891
IL1-4/WTpooled	0.76469	0.834
WT/WTpooled	1.05782	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	1.05156	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.47594
DC3000/delta hrp 6h	0.79797	0.834
DC3000/delta hrp 12h	1.099	1
DC3000/delta hrp 24h	0.88682	0.662

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.19795	0.073
DC3000 delta B/DC3000 delta AB	0.9372	0.483

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.2253	1
Exp 36h	0.95202	0.879
Exp 60h	0.89929	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03003	1
Var 0h	1.05661	0.98
Var 12h I row2-row1	0.94189	0.514
Var 12h NI row2-row1	1.04766	1
Var 36h I row2-row1	1.04317	1
Var 36h NI row2-row1	0.78713	0.361
Var 60h I row2-row1	1.1478	0.562
Var 60h NI row2-row1	1.07379	1
Time course 0hI-0hNI	0.90713	0.356
Time course 12hI-12hNI	1.04674	0.703
Time course 36hI-36hNI	1.32339	0.08
Time course 60hI-60hNI	1.60234	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)	0.97255	0.662
transgenic ySAMdc/azygous control (breaker)	0.70341	0.134
transgenic ySAMdc/azygous control (red)	1.12457	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06778	0.448

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.02755	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.91623	1
Manapal/WT (break)	0.97892	1
Manapal/WT (red)	0.91808	0.36