Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.6.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06679	0.904
27DAP/17DAP	1.05715	0.88
39DAP/27DAP	0.74527	0.41
41DAP/39DAP	1.39919	0.413
42DAP/41DAP	1.08309	0.962
43DAP/42DAP	0.91517	0.841
47DAP/43DAP	1.13346	0.609
52DAP/47DAP	1.03173	0.969
57DAP/52DAP	0.95275	0.845

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98223	0.601
17DAP/reference	1.04624	0.696
27DAP/reference	1.16875	0.077
39DAP/reference	1.11089	0.286
41DAP/reference	1.07037	0.624
42DAP/reference	1.00912	0.587
43DAP/reference	1.15823	0.038
47DAP/reference	1.05635	0.773
52DAP/reference	1.18642	0.217
57DAP/reference	1.11235	0.447

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99242	0.679
27DAP/17DAP	1.0129	1
39DAP/27DAP	0.96356	0.759
41DAP/39DAP	1.35794	0.417
42DAP/41DAP	1.03874	1
43DAP/42DAP	1.05316	0.83
47DAP/43DAP	1.5866	0.082
52DAP/47DAP	1.04349	0.844
57DAP/52DAP	1.40639	0.144
57DAP/7DAP	0.77588	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03705	0.961
17DAP/reference	1.05493	0.896
27DAP/reference	1.11435	0.664
39DAP/reference	0.93134	0.198
41DAP/reference	0.94909	0.412
42DAP/reference	0.98981	0.612
43DAP/reference	0.92357	0.305
47DAP/reference	1.12946	0.106
52DAP/reference	0.9986	0.679
57DAP/reference	1.13329	0.966

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1345	0.308
17DAP/reference	0.81904	0.063
27DAP/reference	1.02662	1
39DAP/reference	0.98059	0.509
41DAP/reference	0.91758	0.141
42DAP/reference	0.96369	0.433
43DAP/reference	1.14414	0.633
47DAP/reference	1.11674	0.065
52DAP/reference	0.99121	0.666
57DAP/reference	0.82687	0.278

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13818	0.251
17DAP/reference	1.01652	0.918
27DAP/reference	0.93943	0.286
39DAP/reference	0.76708	0.058
41DAP/reference	1.14378	0.939
42DAP/reference	0.88326	0.172
43DAP/reference	1.0071	0.858
47DAP/reference	0.8725	0.145
52DAP/reference	1.06834	0.928
57DAP/reference	1.18312	0.164

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.24161	0.878
26DAP/20DAP	0.93907	1
34DAP/26DAP	1.01149	1
51DAP/34DAP	1.09314	0.949
52DAP/51DAP	0.62952	1
53DAP/52DAP	0.94633	0.807
55DAP/53DAP	1.14822	0.834
57DAP/55DAP	0.59192	0.133
62DAP/57DAP	0.54837
68DAP/62DAP	6.10761	0.031
68DAP/14DAP	9.5024	0.077

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.96677	0.52

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.84471	0.03
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.59289
Mature Eggplant/Ripe Tomato	2.99414	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.85761
12-2/M82	N/A	N/A
12-4/M82	0.81909
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	0.88418	1
4-3/M82	N/A	N/A
5-3/M82	1.2589
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.75853	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.95017	0.243
IL2-6/WTpooled	0.88707	1
IL7-5/WTpooled	0.93768	1
IL7-3/WTpooled	0.91448	0.31
IL12-4/WTpooled	0.89662	0.71
IL1-4/WTpooled	0.8849	0.699
WT/WTpooled	1.01971	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	1.00229	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.84863	1
DC3000/delta hrp 6h	0.2503
DC3000/delta hrp 12h	0.97614	1
DC3000/delta hrp 24h	1.16323	0.71

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	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.1078	1
Var 0h	1.00112	1
Var 12h I row2-row1	0.92304	0.948
Var 12h NI row2-row1	1.17949	1
Var 36h I row2-row1	0.98219	1
Var 36h NI row2-row1	0.76376	0.743
Var 60h I row2-row1	1.43266	0.562
Var 60h NI row2-row1	1.25933	0.904
Time course 0hI-0hNI	0.86004	0.967
Time course 12hI-12hNI	0.99336	1
Time course 36hI-36hNI	1.28793	0.056
Time course 60hI-60hNI	1.83723	0.216

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)	1.15531	0.384
transgenic ySAMdc/azygous control (breaker)	0.75919	0.49
transgenic ySAMdc/azygous control (red)	1.12199	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05082	0.1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.0224	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89745	1
Manapal/WT (break)	0.90174	1
Manapal/WT (red)	0.8834	0.181