Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.12.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17716	0.646
27DAP/17DAP	1.0766	1
39DAP/27DAP	0.80712	0.414
41DAP/39DAP	1.13614	0.685
42DAP/41DAP	1.12296	0.997
43DAP/42DAP	1.0249	0.937
47DAP/43DAP	0.98527	0.859
52DAP/47DAP	1.04629	0.983
57DAP/52DAP	1.01216	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.44169	0.055
17DAP/reference	1.19313	0.035
27DAP/reference	0.99583	0.822
39DAP/reference	0.99299	0.885
41DAP/reference	1.18452	0.062
42DAP/reference	1.00804	0.755
43DAP/reference	1.0596	0.445
47DAP/reference	0.89236	0.116
52DAP/reference	0.84354	0.029
57DAP/reference	0.72757	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0207	0.881
27DAP/17DAP	0.92891	0.748
39DAP/27DAP	0.90354	0.251
41DAP/39DAP	1.20642	0.266
42DAP/41DAP	0.99551	0.884
43DAP/42DAP	0.89706	0.336
47DAP/43DAP	1.04768	0.897
52DAP/47DAP	1.1932	0.463
57DAP/52DAP	1.02557	1
57DAP/7DAP	0.76335	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.3505	0.025
17DAP/reference	1.54918	0.007
27DAP/reference	1.58324	0.007
39DAP/reference	1.49679	0.007
41DAP/reference	1.55543	0.02
42DAP/reference	1.6949	0.013
43DAP/reference	1.51553	0.008
47DAP/reference	1.24904	0.468
52DAP/reference	1.48237	0.018
57DAP/reference	1.39484	0.023

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20936	0.141
17DAP/reference	1.36876	0.271
27DAP/reference	1.09036	0.648
39DAP/reference	1.08786	0.725
41DAP/reference	1.03804	1
42DAP/reference	0.9454	0.321
43DAP/reference	1.27363	0.447
47DAP/reference	0.89648	0.099
52DAP/reference	1.04293	0.528
57DAP/reference	1.31709	0.046

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.74778	0.015
17DAP/reference	1.12075	0.467
27DAP/reference	1.27707	0.031
39DAP/reference	1.35967	0.016
41DAP/reference	1.03273	0.637
42DAP/reference	1.16441	0.49
43DAP/reference	1.15062	0.531
47DAP/reference	0.91651	0.296
52DAP/reference	1.15357	0.473
57DAP/reference	0.7561	0.029

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.50936	0.966
26DAP/20DAP	1.04419	0.916
34DAP/26DAP	1.34877	0.819
51DAP/34DAP	1.07402	0.795
52DAP/51DAP	0.90974	1
53DAP/52DAP	0.92238	0.595
55DAP/53DAP	0.84052	0.03
57DAP/55DAP	1.07005	0.71
62DAP/57DAP	1.06716	0.868
68DAP/62DAP	0.74387	0.29
68DAP/14DAP	0.8222	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.77788	0.022

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.92841	0.539
Mature Green Tomato/Ripe Tomato	1.75405	0.048
Immature Eggplant/Mature Eggplant	0.27651	0.032
Ripe Pepper/Ripe Tomato	1.64446	1
Mature Eggplant/Ripe Tomato	6.66808	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.07871	1
12-2/M82	N/A	N/A
12-4/M82	0.94304	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	1.17408
4-1/M82	1.53746
4-3-2/M82	0.98278	1
4-3/M82	1.42228
5-3/M82	1.20831
6-2/M82	N/A	N/A
6-3/M82	0.86982
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.8045

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.28912	0.584
IL7-5/WTpooled	0.75963
IL7-3/WTpooled	0.78871	0.418
IL12-4/WTpooled	0.97639	1
IL1-4/WTpooled	0.95602	1
WT/WTpooled	1.01045	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	1.00295	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97279	1
DC3000/delta hrp 6h	1.04469	1
DC3000/delta hrp 12h	1.01717	1
DC3000/delta hrp 24h	0.78053	0.079

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.83436	0.05
DC3000 delta B/DC3000 delta AB	0.674	0.045

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.80601	1
Exp 36h	0.61356	0.589
Exp 60h	0.67404	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00799	1
Var 0h	1.07487	0.98
Var 12h I row2-row1	0.73436	0.338
Var 12h NI row2-row1	1.0107	1
Var 36h I row2-row1	0.97134	0.805
Var 36h NI row2-row1	1.12722	0.482
Var 60h I row2-row1	0.90448	0.832
Var 60h NI row2-row1	0.91964	0.977
Time course 0hI-0hNI	0.99932	1
Time course 12hI-12hNI	1.01558	0.885
Time course 36hI-36hNI	0.9394	0.26
Time course 60hI-60hNI	0.46786	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)	1.04588	0.408
transgenic ySAMdc/azygous control (breaker)	1.25379	0.248
transgenic ySAMdc/azygous control (red)	0.99885	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.90821	0.07

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.83966	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.28676	0.105
Manapal/WT (break)	2.01894	0.126
Manapal/WT (red)	N/A	N/A