Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.2.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97745	0.823
27DAP/17DAP	1.10189	0.874
39DAP/27DAP	1.16232	0.789
41DAP/39DAP	1.09717	0.939
42DAP/41DAP	1.20992	0.685
43DAP/42DAP	0.99386	0.937
47DAP/43DAP	0.96413	0.859
52DAP/47DAP	0.80004	0.515
57DAP/52DAP	0.81524	0.827

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9603	0.476
17DAP/reference	0.94367	0.342
27DAP/reference	0.97491	0.595
39DAP/reference	1.00951	1
41DAP/reference	0.98896	0.814
42DAP/reference	0.88203	0.022
43DAP/reference	1.05028	0.705
47DAP/reference	1.05266	0.524
52DAP/reference	1.06276	0.663
57DAP/reference	1.04745	0.3

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.2142	0.508
27DAP/17DAP	0.92114	0.821
39DAP/27DAP	0.76941	0.051
41DAP/39DAP	1.16417	0.748
42DAP/41DAP	1.22693	0.478
43DAP/42DAP	1.10598	0.585
47DAP/43DAP	1.02618	0.92
52DAP/47DAP	0.93195	0.797
57DAP/52DAP	1.02991	0.857
57DAP/7DAP	1.20263	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09449	0.638
17DAP/reference	1.16478	0.049
27DAP/reference	1.3425	0.008
39DAP/reference	1.22324	0.033
41DAP/reference	1.32479	0.104
42DAP/reference	1.17073	0.016
43DAP/reference	1.52502	0.01
47DAP/reference	1.4236	0.219
52DAP/reference	1.37354	0.012
57DAP/reference	1.44815	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07691	0.501
17DAP/reference	0.93068	0.326
27DAP/reference	1.04891	0.917
39DAP/reference	0.94831	0.227
41DAP/reference	1.1401	0.285
42DAP/reference	0.99228	0.655
43DAP/reference	1.14033	0.662
47DAP/reference	1.07958	0.264
52DAP/reference	0.83076	0.011
57DAP/reference	0.86419	0.298

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07104	0.433
17DAP/reference	1.23888	0.169
27DAP/reference	1.74836	0.016
39DAP/reference	1.39134	0.01
41DAP/reference	1.26371	0.08
42DAP/reference	1.26121	0.027
43DAP/reference	1.05501	0.828
47DAP/reference	0.98087	0.538
52DAP/reference	1.22349	0.228
57DAP/reference	1.12961	0.167

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.85574	0.961
26DAP/20DAP	1.04862	0.865
34DAP/26DAP	1.11567	1
51DAP/34DAP	1.80785	0.046
52DAP/51DAP	0.8237	1
53DAP/52DAP	1.39662
55DAP/53DAP	0.78531	0.195
57DAP/55DAP	1.09887	0.947
62DAP/57DAP	0.71367	0.466
68DAP/62DAP	1.32453	0.759
68DAP/14DAP	1.15297	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.91481	0.399

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.43928	0.084
Mature Green Tomato/Ripe Tomato	1.78521	0.267
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	3.41921	0.256
Mature Eggplant/Ripe Tomato	0.56623	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.53198	0.591
1-1-2/M82	1.27369	1
12-2/M82	1.04263	1
12-4/M82	0.87477	1
1-3/M82	N/A	N/A
2-1-1/M82	0.93859	1
2-1/M82	0.7835	0.322
2-6/M82	N/A	N/A
3-2/M82	0.96422	1
4-1-1/M82	1.25658
4-1/M82	N/A	N/A
4-3-2/M82	1.23577	0.262
4-3/M82	1.53995	0.268
5-3/M82	1.14902	1
6-2/M82	1.54268
6-3/M82	1.06989	1
7-1/M82	1.13747	1
7-2/M82	1.51841
9-3-2/M82	1.11195	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.6043	0.358
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.94964	0.418
IL12-4/WTpooled	1.05486	0.785
IL1-4/WTpooled	1.85585
WT/WTpooled	1.04306	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	0.89304	0.201

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98374	1
DC3000/delta hrp 6h	1.06921	1
DC3000/delta hrp 12h	0.9431	1
DC3000/delta hrp 24h	0.82139	0.174

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.42994
DC3000 delta B/DC3000 delta AB	0.57001	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.90237	0.328
Exp 36h	0.75417	0.589
Exp 60h	0.65333	0.32

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00445	1
Var 0h	0.84684	1
Var 12h I row2-row1	0.93143	0.856
Var 12h NI row2-row1	1.09359	1
Var 36h I row2-row1	1.06024	1
Var 36h NI row2-row1	0.85141	1
Var 60h I row2-row1	0.87495
Var 60h NI row2-row1	1.00722	1
Time course 0hI-0hNI	0.91406	0.45
Time course 12hI-12hNI	1.02456	0.827
Time course 36hI-36hNI	1.00964	1
Time course 60hI-60hNI	0.35454	0.006

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)	1.13991	0.36
transgenic ySAMdc/azygous control (breaker)	0.66207	0.142
transgenic ySAMdc/azygous control (red)	1.24763	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0318	0.234

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.19141	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.02625	0.083
Manapal/WT (break)	1.54669	0.14
Manapal/WT (red)	1.3432	0.15