Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.5.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.34881	0.63
27DAP/17DAP	1.28848	0.784
39DAP/27DAP	0.82576	0.495
41DAP/39DAP	1.68274	0.31
42DAP/41DAP	0.89104	1
43DAP/42DAP	1.4205	0.501
47DAP/43DAP	1.00715	0.949
52DAP/47DAP	1.30112	0.626
57DAP/52DAP	0.8354	0.869

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85883	0.066
17DAP/reference	0.77694	0.008
27DAP/reference	1.02907	0.953
39DAP/reference	1.01302	0.871
41DAP/reference	1.06315	0.48
42DAP/reference	1.41763	0.08
43DAP/reference	1.10808	0.057
47DAP/reference	1.23534	0.001
52DAP/reference	1.43237	0.024
57DAP/reference	1.08212	0.132

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87346	0.388
27DAP/17DAP	0.87693	0.648
39DAP/27DAP	1.09079	0.646
41DAP/39DAP	1.02797	1
42DAP/41DAP	1.09978	1
43DAP/42DAP	0.94038	0.538
47DAP/43DAP	0.99321	0.971
52DAP/47DAP	0.93408	0.801
57DAP/52DAP	0.85904	0.445
57DAP/7DAP	0.75888	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.52103	0.147
17DAP/reference	2.95267	0.022
27DAP/reference	2.39542	0.007
39DAP/reference	2.83098	0.005
41DAP/reference	2.57558	0.05
42DAP/reference	3.12045	0.007
43DAP/reference	4.57957	0.006
47DAP/reference	1.86454	0.44
52DAP/reference	3.14291	0.007
57DAP/reference	3.15974	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88123	0.124
17DAP/reference	0.74331	0.014
27DAP/reference	0.76606	0.069
39DAP/reference	1.0404	0.978
41DAP/reference	0.94941	0.357
42DAP/reference	0.94915	0.355
43DAP/reference	0.69801	0.036
47DAP/reference	0.85241	0.085
52DAP/reference	0.97881	0.5
57DAP/reference	0.74781	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.8921	0.691
17DAP/reference	1.44514	0.474
27DAP/reference	3.04916	0.035
39DAP/reference	2.47969	0.034
41DAP/reference	2.19072	0.014
42DAP/reference	2.85813	0.009
43DAP/reference	2.93502	0.012
47DAP/reference	1.21158	0.05
52DAP/reference	2.91305	0.098
57DAP/reference	1.67421	0.01

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95325	1
26DAP/20DAP	0.81287	0.317
34DAP/26DAP	0.79	0.619
51DAP/34DAP	1.42733	0.949
52DAP/51DAP	1.27036	0.606
53DAP/52DAP	1.11214	0.797
55DAP/53DAP	1.11596	0.917
57DAP/55DAP	0.72547	0.259
62DAP/57DAP	1.17344	0.569
68DAP/62DAP	1.50405	0.405
68DAP/14DAP	1.4576	0.025

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.33802	0.212

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.58436	0.017
Immature Eggplant/Mature Eggplant	4.69311	0.05
Ripe Pepper/Ripe Tomato	0.11201	0.224
Mature Eggplant/Ripe Tomato	0.34362	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0724	1
1-1-2/M82	0.87803
12-2/M82	N/A	N/A
12-4/M82	1.04954
1-3/M82	1.14052	1
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.84803
3-2/M82	1.7782	0.967
4-1-1/M82	0.70386
4-1/M82	N/A	N/A
4-3-2/M82	1.01398	1
4-3/M82	1.01694	1
5-3/M82	1.14487	1
6-2/M82	1.41749
6-3/M82	0.9521
7-1/M82	N/A	N/A
7-2/M82	0.55829
9-3-2/M82	0.72051	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.86177	0.321
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.6834
IL7-3/WTpooled	0.80174
IL12-4/WTpooled	0.83601	0.566
IL1-4/WTpooled	1.10486	1
WT/WTpooled	0.97479	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	0.89361	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9526	1
DC3000/delta hrp 6h	1.01717	1
DC3000/delta hrp 12h	1.1677	1
DC3000/delta hrp 24h	0.64096	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.42536
DC3000 delta B/DC3000 delta AB	0.54868	0.065

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.05783	1
Exp 36h	0.85608	0.661
Exp 60h	1.1205	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95828	1
Var 0h	1.07955	0.936
Var 12h I row2-row1	1.10926	0.473
Var 12h NI row2-row1	0.96998	0.906
Var 36h I row2-row1	0.89886	1
Var 36h NI row2-row1	1.14204	1
Var 60h I row2-row1	1.41148	1
Var 60h NI row2-row1	1.35995	0.691
Time course 0hI-0hNI	0.93364	0.582
Time course 12hI-12hNI	0.98198	0.906
Time course 36hI-36hNI	0.75654	0.023
Time course 60hI-60hNI	0.29811	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)	0.90873	0.301
transgenic ySAMdc/azygous control (breaker)	1.07097	1
transgenic ySAMdc/azygous control (red)	1.88882	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98366	0.191

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.35738	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.70938	0.083
Manapal/WT (break)	1.13797	1
Manapal/WT (red)	0.96698	0.863