Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.3.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.25186	0.786
27DAP/17DAP	0.80308	0.499
39DAP/27DAP	0.9162	0.594
41DAP/39DAP	1.52586	0.545
42DAP/41DAP	0.84518	1
43DAP/42DAP	0.85295	0.741
47DAP/43DAP	0.82665	0.407
52DAP/47DAP	1.66526	0.22
57DAP/52DAP	0.64181	0.646

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68457	0.025
17DAP/reference	0.57395	0.009
27DAP/reference	1.00204	0.741
39DAP/reference	0.7916	0.056
41DAP/reference	0.72276	0.085
42DAP/reference	1.01408	0.567
43DAP/reference	1.01771	1
47DAP/reference	1.31133	0.19
52DAP/reference	1.53124	0.01
57DAP/reference	1.73851	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96927	0.679
27DAP/17DAP	1.15085	0.465
39DAP/27DAP	0.91065	0.287
41DAP/39DAP	1.23369	0.774
42DAP/41DAP	0.89088	0.404
43DAP/42DAP	0.8107	0.025
47DAP/43DAP	1.10678	0.744
52DAP/47DAP	1.08334	0.785
57DAP/52DAP	1.35729	0.389
57DAP/7DAP	1.8129	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00222	0.758
17DAP/reference	1.15084	0.221
27DAP/reference	0.99551	0.698
39DAP/reference	0.96405	0.307
41DAP/reference	1.05348	0.491
42DAP/reference	1.06306	0.686
43DAP/reference	0.92101	0.21
47DAP/reference	1.04531	0.776
52DAP/reference	0.86185	0.097
57DAP/reference	0.9785	0.494

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74677	0.013
17DAP/reference	0.65164	0.004
27DAP/reference	1.12739	0.648
39DAP/reference	1.46722	0.17
41DAP/reference	1.80869	0.005
42DAP/reference	1.51255	0.007
43DAP/reference	0.93377	0.378
47DAP/reference	1.30796	0.012
52DAP/reference	1.22137	0.032
57DAP/reference	0.92989	0.361

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94948	0.335
17DAP/reference	1.05634	0.887
27DAP/reference	1.09811	0.392
39DAP/reference	1.11487	0.342
41DAP/reference	1.10952	0.188
42DAP/reference	1.31987	0.4
43DAP/reference	1.17163	0.71
47DAP/reference	1.09302	0.585
52DAP/reference	0.99104	0.8
57DAP/reference	3.12845	0.01

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94265	1
26DAP/20DAP	0.93549	1
34DAP/26DAP	1.11772	0.819
51DAP/34DAP	0.9922	0.873
52DAP/51DAP	1.19307	0.503
53DAP/52DAP	1.17726	0.678
55DAP/53DAP	1.16718	0.382
57DAP/55DAP	0.72126	0.213
62DAP/57DAP	1.43351	0.057
68DAP/62DAP	2.66937	0.178
68DAP/14DAP	4.1193	0.016

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.66315	0.025

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	2.92356	0.022
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	7.79464	1
Mature Eggplant/Ripe Tomato	1.46713

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04257	1
1-1-2/M82	1.34586
12-2/M82	1.16232	1
12-4/M82	1.19675	0.694
1-3/M82	0.95893	1
2-1-1/M82	1.05728	1
2-1/M82	N/A	N/A
2-6/M82	0.87438	1
3-2/M82	0.6646
4-1-1/M82	0.84861	1
4-1/M82	1.89273
4-3-2/M82	N/A	N/A
4-3/M82	0.97428
5-3/M82	0.94341	0.49
6-2/M82	0.71843	0.497
6-3/M82	0.99211
7-1/M82	N/A	N/A
7-2/M82	1.04531
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.93833	1
IL2-6/WTpooled	1.05617	0.584
IL7-5/WTpooled	1.07809	0.75
IL7-3/WTpooled	0.90938	0.31
IL12-4/WTpooled	1.02149	0.785
IL1-4/WTpooled	1.0169	1
WT/WTpooled	1.04083	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	0.72512	0.226

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07249	0.914
DC3000/delta hrp 6h	0.99525	0.95
DC3000/delta hrp 12h	0.96493	1
DC3000/delta hrp 24h	0.77651	0.043

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.47137	0.04
DC3000 delta B/DC3000 delta AB	0.54102	0.035

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.77385	0.245
Exp 36h	0.67474	0.406
Exp 60h	0.67823	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96149	1
Var 0h	0.98673	1
Var 12h I row2-row1	0.97674	0.856
Var 12h NI row2-row1	0.9583	0.906
Var 36h I row2-row1	0.79639	0.313
Var 36h NI row2-row1	1.27689	0.276
Var 60h I row2-row1	7.4153	1
Var 60h NI row2-row1	1.1623	0.701
Time course 0hI-0hNI	0.98437	0.973
Time course 12hI-12hNI	0.81084	0.113
Time course 36hI-36hNI	0.61233	0.023
Time course 60hI-60hNI	0.25516	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)	0.97915	0.789
transgenic ySAMdc/azygous control (breaker)	1.92043	1
transgenic ySAMdc/azygous control (red)	1.02266	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.09196	0.261

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.79836	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.5307	1
Manapal/WT (break)	0.94679	1
Manapal/WT (red)	0.71878	0.181