Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.3.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85536	0.331
27DAP/17DAP	1.20404	0.833
39DAP/27DAP	1.02442	0.798
41DAP/39DAP	1.29005	0.638
42DAP/41DAP	1.21043	0.755
43DAP/42DAP	1.0276	1
47DAP/43DAP	1.46446	0.595
52DAP/47DAP	1.01049	0.959
57DAP/52DAP	1.03023	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01329	0.844
17DAP/reference	0.79512	0.007
27DAP/reference	0.85834	0.014
39DAP/reference	0.82021	0.132
41DAP/reference	0.83783	0.009
42DAP/reference	1.05502	1
43DAP/reference	0.8488
47DAP/reference	1.02281	0.817
52DAP/reference	1.09349	1
57DAP/reference	0.67904	0.01

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9874	0.763
27DAP/17DAP	1.08863	0.754
39DAP/27DAP	1.07056	0.548
41DAP/39DAP	1.00321	1
42DAP/41DAP	1.10046	0.675
43DAP/42DAP	0.92302	0.172
47DAP/43DAP	0.99643	0.989
52DAP/47DAP	1.0045	1
57DAP/52DAP	1.02983	0.941
57DAP/7DAP	1.24524	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27525
17DAP/reference	0.93478	0.167
27DAP/reference	0.99128	0.614
39DAP/reference	0.88711	0.011
41DAP/reference	0.97943	0.512
42DAP/reference	1.14766	0.021
43DAP/reference	1.33287	0.022
47DAP/reference	1.21467	0.191
52DAP/reference	1.14376	0.113
57DAP/reference	1.03831	0.698

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08484	0.456
17DAP/reference	0.93248	0.26
27DAP/reference	1.53502	0.028
39DAP/reference	1.36514	0.2
41DAP/reference	1.31838	0.102
42DAP/reference	1.32821	0.133
43DAP/reference	0.99987	0.814
47DAP/reference	1.1276	0.388
52DAP/reference	0.91444	0.012
57DAP/reference	0.81195	0.024

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88124	0.092
17DAP/reference	0.94244	0.477
27DAP/reference	1.02575	0.721
39DAP/reference	1.00834	1
41DAP/reference	0.9697	0.618
42DAP/reference	1.11758	0.55
43DAP/reference	1.43711	0.209
47DAP/reference	0.96933	0.478
52DAP/reference	1.11059	0.558
57DAP/reference	2.7698	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02027	1
26DAP/20DAP	0.93794	0.317
34DAP/26DAP	0.89075	0.834
51DAP/34DAP	0.93476	0.64
52DAP/51DAP	0.96545	1
53DAP/52DAP	1.11215	0.858
55DAP/53DAP	1.04166	1
57DAP/55DAP	0.98895	0.859
62DAP/57DAP	0.81327	0.28
68DAP/62DAP	0.97378	0.834
68DAP/14DAP	1.50564	0.189

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.30489	0.026

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.90249	0.447
Mature Green Tomato/Ripe Tomato	1.8337	0.095
Immature Eggplant/Mature Eggplant	1.66319	0.05
Ripe Pepper/Ripe Tomato	0.79564	0.224
Mature Eggplant/Ripe Tomato	0.54618	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.89813	0.907
1-1-2/M82	1.10253	1
12-2/M82	1.3341	0.61
12-4/M82	0.95066
1-3/M82	0.94832	0.376
2-1-1/M82	1.13508	0.422
2-1/M82	1.05228	1
2-6/M82	1.02408	0.425
3-2/M82	0.91004
4-1-1/M82	0.93737	0.959
4-1/M82	N/A	N/A
4-3-2/M82	1.06481
4-3/M82	1.09814	1
5-3/M82	0.76904	0.447
6-2/M82	1.12125
6-3/M82	N/A	N/A
7-1/M82	0.9503
7-2/M82	1.05788	1
9-3-2/M82	0.99318

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.91069	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.36104
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.9002	0.476
WT/WTpooled	N/A	N/A

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	1.2199	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0582	0.921
DC3000/delta hrp 6h	0.90569	0.95
DC3000/delta hrp 12h	1.05094	1
DC3000/delta hrp 24h	1.07358	0.595

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.65039	0.024
DC3000 delta B/DC3000 delta AB	1.01627	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01822	1
Exp 36h	1.37321	0.693
Exp 60h	1.3873	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98188	1
Var 0h	0.99947	1
Var 12h I row2-row1	0.99598	1
Var 12h NI row2-row1	0.91459	0.627
Var 36h I row2-row1	1.2813	0.601
Var 36h NI row2-row1	1.09743	1
Var 60h I row2-row1	0.95869	0.292
Var 60h NI row2-row1	1.07548	0.904
Time course 0hI-0hNI	0.97678	0.906
Time course 12hI-12hNI	0.87646	0.104
Time course 36hI-36hNI	0.80347	0.023
Time course 60hI-60hNI	0.45235	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)	1.05468	0.372
transgenic ySAMdc/azygous control (breaker)	0.55342	0.15
transgenic ySAMdc/azygous control (red)	0.94395	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08775	0.045

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.48274	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.08126	1
Manapal/WT (break)	1.46555	0.183
Manapal/WT (red)	1.06449	1