Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.9.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17109	0.812
27DAP/17DAP	1.13785	0.927
39DAP/27DAP	1.0886	0.972
41DAP/39DAP	1.15864	0.447
42DAP/41DAP	1.38053	0.536
43DAP/42DAP	1.21069	0.956
47DAP/43DAP	1.95434	0.609
52DAP/47DAP	1.0077	0.859
57DAP/52DAP	1.51256	0.853

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8648	0.194
17DAP/reference	0.94541	0.474
27DAP/reference	0.95442	0.497
39DAP/reference	1.02098	0.842
41DAP/reference	1.06096	0.48
42DAP/reference	0.90002	0.069
43DAP/reference	1.17226	0.163
47DAP/reference	1.01012	0.674
52DAP/reference	1.21805	0.498
57DAP/reference	1.24994	0.01

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.37714	0.164
27DAP/17DAP	0.98881	0.943
39DAP/27DAP	0.88757	0.405
41DAP/39DAP	1.03415	0.914
42DAP/41DAP	1.00309	0.884
43DAP/42DAP	0.96439	0.709
47DAP/43DAP	0.94592	0.447
52DAP/47DAP	1.08388	0.831
57DAP/52DAP	0.9339	0.75
57DAP/7DAP	1.1719

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93226	0.445
17DAP/reference	1.21671	0.147
27DAP/reference	1.46884	0.01
39DAP/reference	1.21754	0.157
41DAP/reference	1.36987	0.026
42DAP/reference	1.50065	0.009
43DAP/reference	1.20201	0.212
47DAP/reference	1.10342	0.504
52DAP/reference	0.96714	0.523
57DAP/reference	1.26	0.214

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86406	0.257
17DAP/reference	0.68342	0.005
27DAP/reference	1.01608	1
39DAP/reference	1.04195	0.722
41DAP/reference	1.32608	0.058
42DAP/reference	0.85747	0.169
43DAP/reference	0.85346	0.468
47DAP/reference	0.92193	0.194
52DAP/reference	1.17091	0.135
57DAP/reference	1.18345	0.146

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99014	0.653
17DAP/reference	0.85043	0.21
27DAP/reference	1.13528	0.207
39DAP/reference	0.98302	0.643
41DAP/reference	1.0589	0.674
42DAP/reference	1.06887	0.635
43DAP/reference	1.16843	0.123
47DAP/reference	0.93774	0.335
52DAP/reference	1.5966	0.209
57DAP/reference	1.02912	0.858

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91582	1
26DAP/20DAP	0.97839
34DAP/26DAP	0.97915	0.954
51DAP/34DAP	1.22937	0.496
52DAP/51DAP	1.02494	1
53DAP/52DAP	1.16752	0.662
55DAP/53DAP	0.79204	0.13
57DAP/55DAP	1.00927	0.955
62DAP/57DAP	0.77816	0.028
68DAP/62DAP	0.647	0.227
68DAP/14DAP	0.6618	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.49094	0.039

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.77976
Immature Eggplant/Mature Eggplant	2.73494
Ripe Pepper/Ripe Tomato	1.51721
Mature Eggplant/Ripe Tomato	1.34174

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01185	1
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.95391	1
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	N/A	N/A
4-3/M82	0.9938	1
5-3/M82	1.16949	0.572
6-2/M82	N/A	N/A
6-3/M82	1.32867
7-1/M82	N/A	N/A
7-2/M82	0.84691
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.91912	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.20432	0.362
IL12-4/WTpooled	0.96498	1
IL1-4/WTpooled	1.00722
WT/WTpooled	0.90634	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	0.76502	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11874	0.921
DC3000/delta hrp 6h	1.58387	1
DC3000/delta hrp 12h	0.84402	1
DC3000/delta hrp 24h	1.23653	0.483

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	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	1.81747	1
Exp 60h	0.92149	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.06011	1
Var 0h	0.98637	1
Var 12h I row2-row1	1.52478	0.654
Var 12h NI row2-row1	1.41054	1
Var 36h I row2-row1	0.92544	1
Var 36h NI row2-row1	0.98682	0.852
Var 60h I row2-row1	0.88534	0.287
Var 60h NI row2-row1	0.93518	0.904
Time course 0hI-0hNI	0.94886	0.799
Time course 12hI-12hNI	0.90844	0.501
Time course 36hI-36hNI	0.85539	0.056
Time course 60hI-60hNI	1.52408	0.426

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)	1.07121	0.571
transgenic ySAMdc/azygous control (breaker)	1.69775	0.161
transgenic ySAMdc/azygous control (red)	1.0454	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.15487	0.057

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.75111	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.63968	0.172
Manapal/WT (break)	0.8426	1
Manapal/WT (red)	1.25707	0.413