Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.2.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81411	0.244
27DAP/17DAP	0.79104	0.483
39DAP/27DAP	0.63003	0.364
41DAP/39DAP	1.23109	0.58
42DAP/41DAP	1.51524	0.353
43DAP/42DAP	1.07464	1
47DAP/43DAP	1.18397	0.793
52DAP/47DAP	0.84597	0.63
57DAP/52DAP	1.11414	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0511	0.17
17DAP/reference	1.09471	0.843
27DAP/reference	0.91559	0.249
39DAP/reference	0.9221	0.174
41DAP/reference	0.99989	1
42DAP/reference	0.81241	0.002
43DAP/reference	0.96331	0.48
47DAP/reference	0.83136	0.021
52DAP/reference	0.9136	0.223
57DAP/reference	1.10108	0.463

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8996	0.47
27DAP/17DAP	0.92392	0.58
39DAP/27DAP	0.97325	0.87
41DAP/39DAP	1.00096	1
42DAP/41DAP	1.20896	0.095
43DAP/42DAP	1.21335	0.094
47DAP/43DAP	1.09243	0.758
52DAP/47DAP	0.84803	0.237
57DAP/52DAP	0.89635	0.467
57DAP/7DAP	0.83875	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.5248	0.052
17DAP/reference	1.88104	0.007
27DAP/reference	2.1904	0.008
39DAP/reference	2.64655	0.005
41DAP/reference	2.68417	0.013
42DAP/reference	2.65812	0.006
43DAP/reference	2.53613	0.006
47DAP/reference	1.80981	0.36
52DAP/reference	2.36497	0.007
57DAP/reference	2.14786	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00846	0.93
17DAP/reference	0.89221	0.077
27DAP/reference	0.85226	0.119
39DAP/reference	0.88729	0.097
41DAP/reference	0.9717	0.422
42DAP/reference	0.86587	0.028
43DAP/reference	0.78168	0.022
47DAP/reference	0.8807	0.053
52DAP/reference	0.94436	0.327
57DAP/reference	0.60982	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.47386	0.044
17DAP/reference	1.38366	0.241
27DAP/reference	1.77022	0.017
39DAP/reference	1.75852	0.011
41DAP/reference	2.07737	0.011
42DAP/reference	1.55731	0.039
43DAP/reference	1.82736	0.027
47DAP/reference	1.10511	0.48
52DAP/reference	1.48584	0.172
57DAP/reference	1.26729	0.153

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03982	1
26DAP/20DAP	1.0781	0.744
34DAP/26DAP	1.12489	0.819
51DAP/34DAP	1.54168	0.293
52DAP/51DAP	0.83711	1
53DAP/52DAP	0.8386	0.475
55DAP/53DAP	0.87726	0.544
57DAP/55DAP	1.0154	1
62DAP/57DAP	1.00537	1
68DAP/62DAP	1.53999	0.014
68DAP/14DAP	1.33898	0.067

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.74224	0.038

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.027	0.908
Mature Green Tomato/Ripe Tomato	1.55608	0.185
Immature Eggplant/Mature Eggplant	0.57451
Ripe Pepper/Ripe Tomato	3.54124	0.256
Mature Eggplant/Ripe Tomato	6.80681	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.45466
12-2/M82	N/A	N/A
12-4/M82	0.78555	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	0.80829
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.97768
4-3/M82	N/A	N/A
5-3/M82	1.64093
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	1.50156

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.57649	0.243
IL2-6/WTpooled	0.91617	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.14492	0.362
IL12-4/WTpooled	0.94854	1
IL1-4/WTpooled	0.70658	0.457
WT/WTpooled	0.99017	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	0.9232	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0269	0.921
DC3000/delta hrp 6h	1.27509	1
DC3000/delta hrp 12h	1.36163	1
DC3000/delta hrp 24h	0.43094	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.668	0.024
DC3000 delta B/DC3000 delta AB	0.65703	0.026

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.92069	1
Exp 36h	0.72778	0.449
Exp 60h	0.60774	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00189	1
Var 0h	0.88877	0.933
Var 12h I row2-row1	0.85607	0.344
Var 12h NI row2-row1	0.98455	0.906
Var 36h I row2-row1	0.97908	1
Var 36h NI row2-row1	1.26756	0.482
Var 60h I row2-row1	1.41325	1
Var 60h NI row2-row1	1.16082	0.904
Time course 0hI-0hNI	0.98536	0.97
Time course 12hI-12hNI	0.96376	0.745
Time course 36hI-36hNI	0.84753	0.034
Time course 60hI-60hNI	0.30928	0.005

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)	0.88154	0.246
transgenic ySAMdc/azygous control (breaker)	0.80018	0.173
transgenic ySAMdc/azygous control (red)	1.30718	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98506	0.459

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.24613	0.228

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.55497	0.083
Manapal/WT (break)	2.12551	0.13
Manapal/WT (red)	1.63833	0.164