Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.9.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92904	0.522
27DAP/17DAP	1.13538	0.849
39DAP/27DAP	1.0152	1
41DAP/39DAP	0.8159	0.33
42DAP/41DAP	1.00812	1
43DAP/42DAP	1.1495	0.823
47DAP/43DAP	1.07798	0.746
52DAP/47DAP	0.90013	0.702
57DAP/52DAP	1.0703	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.36979	0.038
17DAP/reference	1.20734	0.306
27DAP/reference	1.00593	0.885
39DAP/reference	1.08383	0.262
41DAP/reference	1.10227	0.552
42DAP/reference	1.43653	0.043
43DAP/reference	1.0999	0.495
47DAP/reference	1.19203	0.114
52DAP/reference	1.05056	0.912
57DAP/reference	0.90772	0.124

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97691	0.716
27DAP/17DAP	1.03985	0.909
39DAP/27DAP	1.22542	0.378
41DAP/39DAP	0.88732	0.434
42DAP/41DAP	1.16037	0.495
43DAP/42DAP	1.06146	0.446
47DAP/43DAP	1.07063	0.756
52DAP/47DAP	0.94814	0.79
57DAP/52DAP	1.16377	0.368
57DAP/7DAP	1.28658	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20145	0.117
17DAP/reference	0.94058	0.338
27DAP/reference	1.11198	0.371
39DAP/reference	0.93938	0.198
41DAP/reference	1.09683	0.27
42DAP/reference	1.1877	0.174
43DAP/reference	1.44385	0.009
47DAP/reference	1.31049	0.051
52DAP/reference	1.14643	0.636
57DAP/reference	0.94376	0.328

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23729	0.129
17DAP/reference	1.32548	0.426
27DAP/reference	1.41944	0.02
39DAP/reference	1.13347	0.489
41DAP/reference	1.37071	0.362
42DAP/reference	1.36862	0.021
43DAP/reference	1.3945	0.112
47DAP/reference	1.45535	0.008
52DAP/reference	1.09978	0.3
57DAP/reference	1.30317	0.091

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01579	1
17DAP/reference	1.01841	0.763
27DAP/reference	0.92384	0.442
39DAP/reference	0.9865	0.643
41DAP/reference	0.94528	0.459
42DAP/reference	1.12465	0.54
43DAP/reference	1.15491	0.688
47DAP/reference	1.43077	0.032
52DAP/reference	1.46948	0.237
57DAP/reference	1.22744	0.098

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1773	0.966
26DAP/20DAP	0.95808	1
34DAP/26DAP	1.27367	0.819
51DAP/34DAP	1.80082	0.03
52DAP/51DAP	0.65631	0.079
53DAP/52DAP	1.52325	0.072
55DAP/53DAP	0.68404	0.102
57DAP/55DAP	1.19821	0.694
62DAP/57DAP	1.35138	0.723
68DAP/62DAP	0.7398	0.378
68DAP/14DAP	0.82835	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.58966	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.04914	1
Immature Eggplant/Mature Eggplant	0.87788
Ripe Pepper/Ripe Tomato	1.17775	1
Mature Eggplant/Ripe Tomato	1.27705	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.937
1-1-2/M82	1.10357	1
12-2/M82	N/A	N/A
12-4/M82	1.01327	1
1-3/M82	N/A	N/A
2-1-1/M82	1.13161
2-1/M82	N/A	N/A
2-6/M82	1.31561
3-2/M82	0.92369
4-1-1/M82	N/A	N/A
4-1/M82	0.9967
4-3-2/M82	1.06786	1
4-3/M82	N/A	N/A
5-3/M82	1.01973	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.99156
7-2/M82	0.96298	1
9-3-2/M82	1.25186	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.89214	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.30444	1
IL12-4/WTpooled	1.22831	0.546
IL1-4/WTpooled	1.03615	1
WT/WTpooled	0.9703	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	0.71682	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94511	1
DC3000/delta hrp 6h	1.19298	1
DC3000/delta hrp 12h	1.07218	1
DC3000/delta hrp 24h	0.93116	0.464

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.50241	0.03
DC3000 delta B/DC3000 delta AB	0.53154	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0314	1
Exp 36h	0.919	0.82
Exp 60h	0.69909	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99321	1
Var 0h	1.23734	0.936
Var 12h I row2-row1	0.95588	0.77
Var 12h NI row2-row1	0.90969	0.82
Var 36h I row2-row1	1.1775	0.908
Var 36h NI row2-row1	1.18154	0.482
Var 60h I row2-row1	0.90694	0.832
Var 60h NI row2-row1	1.097	1
Time course 0hI-0hNI	0.84474	0.142
Time course 12hI-12hNI	0.96757	0.815
Time course 36hI-36hNI	0.88297	0.073
Time course 60hI-60hNI	0.54664	0.007

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)	0.90124	0.485
transgenic ySAMdc/azygous control (breaker)	1.17582	1
transgenic ySAMdc/azygous control (red)	1.06472	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.11381	0.142

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.02138	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.24103	0.096
Manapal/WT (break)	1.58287	0.381
Manapal/WT (red)	1.31378	0.126