Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.16.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.71076	0.156
27DAP/17DAP	0.85993	0.637
39DAP/27DAP	1.69247	0.542
41DAP/39DAP	0.99459	0.798
42DAP/41DAP	0.42599	0.262
43DAP/42DAP	0.88349	0.801
47DAP/43DAP	0.57055	0.074
52DAP/47DAP	1.50619	0.247
57DAP/52DAP	1.11016	0.985

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.46469	0.006
17DAP/reference	1.13133	0.764
27DAP/reference	0.78063	0.089
39DAP/reference	0.8619	0.17
41DAP/reference	0.84148	0.085
42DAP/reference	1.01305	0.707
43DAP/reference	0.77115	0.051
47DAP/reference	0.72234	0.003
52DAP/reference	0.73783	0.051
57DAP/reference	0.94564	0.358

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.3787	0.024
27DAP/17DAP	1.96066	0.023
39DAP/27DAP	0.45842	0.03
41DAP/39DAP	1.46942	0.371
42DAP/41DAP	0.89457	0.447
43DAP/42DAP	1.80219	0.021
47DAP/43DAP	1.06747	0.817
52DAP/47DAP	0.68464	0.174
57DAP/52DAP	1.59248	0.047
57DAP/7DAP	0.65138	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.05309	0.024
17DAP/reference	1.61609	0.032
27DAP/reference	1.3312	0.131
39DAP/reference	0.834	0.043
41DAP/reference	1.34846	0.009
42DAP/reference	1.06282	0.889
43DAP/reference	1.22624	0.256
47DAP/reference	1.34271	0.079
52DAP/reference	1.16979	0.159
57DAP/reference	0.82773	0.038

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.72996	0.043
17DAP/reference	1.35915	0.052
27DAP/reference	1.49359	0.013
39DAP/reference	1.09412	0.556
41DAP/reference	1.22451	0.035
42DAP/reference	1.53303	0.007
43DAP/reference	0.78828	0.075
47DAP/reference	0.94843	0.27
52DAP/reference	0.92848	0.22
57DAP/reference	0.67353	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.95302	0.015
17DAP/reference	1.22995	0.294
27DAP/reference	1.38436	0.014
39DAP/reference	1.02544	0.836
41DAP/reference	0.85752	0.046
42DAP/reference	0.83055	0.028
43DAP/reference	0.7297	0.036
47DAP/reference	0.59098	0.005
52DAP/reference	0.62819	0.06
57DAP/reference	0.79038	0.021

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.7051	0.585
26DAP/20DAP	2.62331	0.097
34DAP/26DAP	0.72826	0.095
51DAP/34DAP	0.98562	0.863
52DAP/51DAP	1.0427	0.848
53DAP/52DAP	1.00423	1
55DAP/53DAP	0.84432	0.094
57DAP/55DAP	1.99428	0.424
62DAP/57DAP	0.67838	0.088
68DAP/62DAP	1.11564	0.792
68DAP/14DAP	3.38052	0.074

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.72258	0.035

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.63167	0.058
Mature Green Tomato/Ripe Tomato	1.87316	0.015
Immature Eggplant/Mature Eggplant	0.86617	0.1
Ripe Pepper/Ripe Tomato	1.4347	1
Mature Eggplant/Ripe Tomato	2.44396	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.10838
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.18401	0.694
1-3/M82	2.25384
2-1-1/M82	0.97447	1
2-1/M82	0.81283
2-6/M82	0.61805
3-2/M82	1.45931
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.92922	1
4-3/M82	0.89176	0.72
5-3/M82	0.9984	1
6-2/M82	3.37722	0.235
6-3/M82	1.01541	1
7-1/M82	1.47659
7-2/M82	N/A	N/A
9-3-2/M82	0.83914

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
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	0.95631	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98793	1
DC3000/delta hrp 6h	0.80717	0.95
DC3000/delta hrp 12h	0.8798	1
DC3000/delta hrp 24h	2.14586	0.03

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.84482	0.062
DC3000 delta B/DC3000 delta AB	0.78838	0.037

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.91012	0.265
Exp 36h	1.08501	1
Exp 60h	0.84213	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03922	1
Var 0h	1.12459	0.936
Var 12h I row2-row1	1.24197	0.58
Var 12h NI row2-row1	1.03918	1
Var 36h I row2-row1	0.75084	0.805
Var 36h NI row2-row1	1.26285	1
Var 60h I row2-row1	0.81459	0.285
Var 60h NI row2-row1	1.12229	0.904
Time course 0hI-0hNI	1.02454	0.867
Time course 12hI-12hNI	0.9576	0.698
Time course 36hI-36hNI	0.89051	0.119
Time course 60hI-60hNI	0.74871	0.015

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)	1.10698	0.347
transgenic ySAMdc/azygous control (breaker)	0.61847	0.139
transgenic ySAMdc/azygous control (red)	0.91451	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01294	1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01614	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.03772	1
Manapal/WT (break)	0.69829	0.333
Manapal/WT (red)	0.8413	0.315