Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.8.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.2877	0.67
27DAP/17DAP	1.25048	0.857
39DAP/27DAP	3.10886	0.02
41DAP/39DAP	2.38617	0.212
42DAP/41DAP	3.82338	0.02
43DAP/42DAP	2.30177	0.756
47DAP/43DAP	0.76847	0.25
52DAP/47DAP	0.50677	0.04
57DAP/52DAP	1.4616	0.853

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05189	0.872
17DAP/reference	1.30463	0.019
27DAP/reference	1.09135	0.587
39DAP/reference	1.08306	0.581
41DAP/reference	1.19209	0.093
42DAP/reference	0.96177	0.268
43DAP/reference	0.99162	0.82
47DAP/reference	0.98532	0.445
52DAP/reference	0.88524	0.195
57DAP/reference	0.90583	0.124

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15582	0.558
27DAP/17DAP	0.97553	0.943
39DAP/27DAP	3.03505	0.032
41DAP/39DAP	0.33918	0.013
42DAP/41DAP	2.46484	0.002
43DAP/42DAP	3.93942	0.013
47DAP/43DAP	0.90482	0.597
52DAP/47DAP	1.04593	0.975
57DAP/52DAP	1.17848	0.493
57DAP/7DAP	3.21798	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85945	0.138
17DAP/reference	0.83993	0.124
27DAP/reference	0.96448	0.375
39DAP/reference	0.96059	0.411
41DAP/reference	1.02888	0.811
42DAP/reference	0.98534	0.582
43DAP/reference	0.89	0.051
47DAP/reference	0.73817	0.066
52DAP/reference	0.92625	0.232
57DAP/reference	0.91351	0.17

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20227	0.048
17DAP/reference	1.13645	0.518
27DAP/reference	0.88975	0.203
39DAP/reference	0.91444	0.322
41DAP/reference	0.82325	0.07
42DAP/reference	1.123	0.555
43DAP/reference	1.169	0.453
47DAP/reference	0.9796	0.527
52DAP/reference	0.90039	0.22
57DAP/reference	1.0942	0.827

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87654	0.197
17DAP/reference	1.02947	0.814
27DAP/reference	0.84082	0.036
39DAP/reference	0.93824	0.328
41DAP/reference	0.81854	0.264
42DAP/reference	0.92942	0.445
43DAP/reference	0.74068	0.143
47DAP/reference	0.96946	0.509
52DAP/reference	0.90943	0.472
57DAP/reference	0.86734	0.078

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95159	1
26DAP/20DAP	0.82105
34DAP/26DAP	0.90229	0.954
51DAP/34DAP	0.99624
52DAP/51DAP	1.06438
53DAP/52DAP	0.93175	0.772
55DAP/53DAP	1.12956	0.869
57DAP/55DAP	1.01894	0.955
62DAP/57DAP	1.13704	0.767
68DAP/62DAP	0.99352	0.863
68DAP/14DAP	0.84486	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	27.8294	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.1662	0.016
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.82288	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.40302
1-1-2/M82	1.62382
12-2/M82	N/A	N/A
12-4/M82	1.43988	1
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	0.97528
4-1-1/M82	N/A	N/A
4-1/M82	1.28817
4-3-2/M82	1.02073	1
4-3/M82	N/A	N/A
5-3/M82	0.97917	0.642
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.80838
7-2/M82	N/A	N/A
9-3-2/M82	0.77012	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.17513	0.365
IL2-6/WTpooled	1.07361	0.659
IL7-5/WTpooled	1.32956	1
IL7-3/WTpooled	1.04144	1
IL12-4/WTpooled	0.95068	1
IL1-4/WTpooled	1.13734	1
WT/WTpooled	1.01118	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	1.03986	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.28677	0.921
DC3000/delta hrp 6h	0.28108
DC3000/delta hrp 12h	0.74569	1
DC3000/delta hrp 24h	1.15438	0.553

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	1.02684	1
Var 0h	1.07011	0.274
Var 12h I row2-row1	0.83811	0.514
Var 12h NI row2-row1	1.41154	1
Var 36h I row2-row1	1.17038	0.908
Var 36h NI row2-row1	0.51487	0.549
Var 60h I row2-row1	0.84273	0.582
Var 60h NI row2-row1	0.76042	0.572
Time course 0hI-0hNI	1.02542	0.852
Time course 12hI-12hNI	0.96744	0.815
Time course 36hI-36hNI	1.72857	0.01
Time course 60hI-60hNI	6.8246	0.008

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)	10.8313	0.748
transgenic ySAMdc/azygous control (breaker)	1.07897	1
transgenic ySAMdc/azygous control (red)	1.01331	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96514	0.313

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.0603	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.73582	1
Manapal/WT (break)	1.10394	1
Manapal/WT (red)	0.75488	0.181