Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.17.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17188	0.997
27DAP/17DAP	2.57203	0.086
39DAP/27DAP	4.29285	0.208
41DAP/39DAP	1.75787	0.293
42DAP/41DAP	3.66082	0.019
43DAP/42DAP	2.06955	0.84
47DAP/43DAP	0.89575	0.645
52DAP/47DAP	0.51758	0.048
57DAP/52DAP	1.55748	0.941

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1743	0.846
17DAP/reference	0.84654	0.091
27DAP/reference	1.02898	1
39DAP/reference	1.02412	0.828
41DAP/reference	1.00339	1
42DAP/reference	1.25089	0.015
43DAP/reference	1.06273	0.838
47DAP/reference	1.34609	0.022
52DAP/reference	1.45981	0.024
57DAP/reference	1.26695	0.073

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.84975	0.076
27DAP/17DAP	0.98971	0.943
39DAP/27DAP	8.55993	0.022
41DAP/39DAP	0.18972	0.013
42DAP/41DAP	3.91417	0.002
43DAP/42DAP	5.33954	0.013
47DAP/43DAP	0.83275	0.29
52DAP/47DAP	1.04017	0.951
57DAP/52DAP	1.20699	0.36
57DAP/7DAP	13.9359	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.12787	0.052
17DAP/reference	0.11894	0.011
27DAP/reference	0.22465	0.01
39DAP/reference	0.5576	0.02
41DAP/reference	0.4651	0.029
42DAP/reference	1.0377	0.458
43DAP/reference	2.14057	0.013
47DAP/reference	1.97277	0.318
52DAP/reference	0.69589	0.021
57DAP/reference	0.67468	0.011

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88233	0.532
17DAP/reference	0.94956	0.51
27DAP/reference	0.75275	0.111
39DAP/reference	0.95961	0.455
41DAP/reference	1.02413	0.702
42DAP/reference	1.02524	1
43DAP/reference	0.89001	0.269
47DAP/reference	0.86436	0.039
52DAP/reference	0.87373	0.131
57DAP/reference	0.74299	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.37673	0.047
17DAP/reference	2.12154	0.286
27DAP/reference	0.24206	0.031
39DAP/reference	0.39714	0.017
41DAP/reference	0.61926	0.046
42DAP/reference	4.5193	0.007
43DAP/reference	4.17184	0.008
47DAP/reference	1.03531	0.687
52DAP/reference	2.92201	0.1
57DAP/reference	1.12857	0.204

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.66355	0.65
26DAP/20DAP	0.84401	1
34DAP/26DAP	1.20834	1
51DAP/34DAP	0.80839	0.286
52DAP/51DAP	9.22422	0.413
53DAP/52DAP	0.9617	0.854
55DAP/53DAP	1.18761	1
57DAP/55DAP	1.26728	0.927
62DAP/57DAP	1.098	1
68DAP/62DAP	1.00707	1
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	68.0547	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	0.14623	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.0045
Mature Eggplant/Ripe Tomato	0.15751	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.73712
1-1-2/M82	1.32462	1
12-2/M82	1.23315	1
12-4/M82	1.25693	1
1-3/M82	1.83472	0.277
2-1-1/M82	0.80026	0.465
2-1/M82	0.7921	0.74
2-6/M82	0.62286
3-2/M82	0.98715	1
4-1-1/M82	0.63623
4-1/M82	1.12669	1
4-3-2/M82	0.84914	1
4-3/M82	1.05871	1
5-3/M82	0.93326
6-2/M82	1.10169	1
6-3/M82	0.67373	0.232
7-1/M82	0.92691	0.803
7-2/M82	1.1121
9-3-2/M82	0.83201	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.44532	0.243
IL2-6/WTpooled	0.82266	1
IL7-5/WTpooled	0.72706	1
IL7-3/WTpooled	0.36669	0.294
IL12-4/WTpooled	0.88705	1
IL1-4/WTpooled	0.71966	0.562
WT/WTpooled	1.03845	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	1.17579	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02184	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.5947
DC3000/delta hrp 24h	0.5105	0.054

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.41624
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95889	1
Var 0h	1.88835	0.98
Var 12h I row2-row1	1.31118	0.406
Var 12h NI row2-row1	1.04957	1
Var 36h I row2-row1	0.98189	1
Var 36h NI row2-row1	0.94391	0.791
Var 60h I row2-row1	0.98952	1
Var 60h NI row2-row1	0.7559	1
Time course 0hI-0hNI	0.82221	0.623
Time course 12hI-12hNI	0.92947	0.436
Time course 36hI-36hNI	0.89287	0.065
Time course 60hI-60hNI	1.27138	0.16

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	1.11625	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.39138	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	0.81318	0.333
Manapal/WT (red)	1.0165	1