Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.8.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1996	0.561
27DAP/17DAP	1.14391	0.841
39DAP/27DAP	1.05744	1
41DAP/39DAP	0.96634	0.825
42DAP/41DAP	1.06517	0.938
43DAP/42DAP	1.05602	1
47DAP/43DAP	1.3898	0.497
52DAP/47DAP	1.12919	0.964
57DAP/52DAP	0.96567	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83523	0.149
17DAP/reference	1.12152	0.355
27DAP/reference	2.05301	0.007
39DAP/reference	1.42156	0.072
41DAP/reference	1.25616	0.047
42DAP/reference	0.8897	0.196
43DAP/reference	0.95598	0.555
47DAP/reference	0.86294	0.012
52DAP/reference	0.8174	0.03
57DAP/reference	0.8831	0.082

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.56478	0.036
27DAP/17DAP	0.92063	0.312
39DAP/27DAP	1.40083	0.082
41DAP/39DAP	0.75213	0.169
42DAP/41DAP	1.03508	0.947
43DAP/42DAP	1.02523	0.788
47DAP/43DAP	0.92843	0.286
52DAP/47DAP	1.09783	0.666
57DAP/52DAP	0.90153	0.395
57DAP/7DAP	1.51157	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78239	0.061
17DAP/reference	1.08559	0.437
27DAP/reference	1.15331	0.073
39DAP/reference	1.52701	0.006
41DAP/reference	1.24025	0.445
42DAP/reference	1.97082	0.007
43DAP/reference	2.44608	0.006
47DAP/reference	1.45923	0.43
52DAP/reference	2.04272	0.008
57DAP/reference	2.24968	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.73977	0.015
17DAP/reference	0.85759	0.134
27DAP/reference	0.77551	0.033
39DAP/reference	0.72307	0.14
41DAP/reference	0.86395	0.071
42DAP/reference	0.79588	0.025
43DAP/reference	0.77447	0.048
47DAP/reference	0.8865	0.094
52DAP/reference	0.77595	0.012
57DAP/reference	0.87436	0.18

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.46629	0.026
17DAP/reference	0.87579	0.21
27DAP/reference	1.08422	0.392
39DAP/reference	1.48268	0.016
41DAP/reference	1.17491	0.018
42DAP/reference	1.00075	0.816
43DAP/reference	0.984	0.639
47DAP/reference	0.71323	0.006
52DAP/reference	1.0412	0.821
57DAP/reference	0.90198	0.234

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00987	1
26DAP/20DAP	0.78152	0.512
34DAP/26DAP	1.05179	1
51DAP/34DAP	1.04627	1
52DAP/51DAP	0.83891	1
53DAP/52DAP	1.26966	0.082
55DAP/53DAP	0.91321	0.445
57DAP/55DAP	1.05796	0.975
62DAP/57DAP	1.0539	0.257
68DAP/62DAP	0.80045	0.055
68DAP/14DAP	1.89271	0.17

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.65521	0.028

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.39631	0.058
Mature Green Tomato/Ripe Tomato	2.37663	0.015
Immature Eggplant/Mature Eggplant	1.1963	0.054
Ripe Pepper/Ripe Tomato	1.23855	1
Mature Eggplant/Ripe Tomato	1.15001	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.93368	0.944
1-1-2/M82	1.16063	1
12-2/M82	1.07307	1
12-4/M82	1.04723	1
1-3/M82	2.44331	0.248
2-1-1/M82	0.85055	0.683
2-1/M82	0.69273	0.325
2-6/M82	1.27335	0.505
3-2/M82	1.02728	1
4-1-1/M82	1.49574	1
4-1/M82	1.02254	1
4-3-2/M82	1.26617	1
4-3/M82	0.85333	0.611
5-3/M82	1.07979	1
6-2/M82	N/A	N/A
6-3/M82	1.11923	1
7-1/M82	1.32921	0.598
7-2/M82	1.33097	1
9-3-2/M82	1.27512	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.4344	0.427
IL7-5/WTpooled	2.57011
IL7-3/WTpooled	0.73848	0.294
IL12-4/WTpooled	0.72113	0.497
IL1-4/WTpooled	1.2103
WT/WTpooled	1.00759	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	0.95044	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.12072	0.914
DC3000/delta hrp 6h	1.13458	1
DC3000/delta hrp 12h	1.30543	1
DC3000/delta hrp 24h	0.60644	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.83734	0.132
DC3000 delta B/DC3000 delta AB	0.87461	0.178

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.01169	1
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	1.02505	1
Var 0h	1.13573	0.98
Var 12h I row2-row1	0.89373	0.338
Var 12h NI row2-row1	0.85343	0.466
Var 36h I row2-row1	0.74838	1
Var 36h NI row2-row1	1.22575	1
Var 60h I row2-row1	1.24714	0.523
Var 60h NI row2-row1	1.11951	0.904
Time course 0hI-0hNI	1.05089	0.799
Time course 12hI-12hNI	0.89328	0.182
Time course 36hI-36hNI	0.77298	0.023
Time course 60hI-60hNI	0.29336	0.026

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)	0.92949	0.377
transgenic ySAMdc/azygous control (breaker)	0.85535	0.49
transgenic ySAMdc/azygous control (red)	0.9061	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.58526	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.18424	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.45318	0.172
Manapal/WT (break)	0.54417	0.255
Manapal/WT (red)	1.12204	1