Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.16.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.31238	0.827
27DAP/17DAP	0.99876	1
39DAP/27DAP	1.24277	0.735
41DAP/39DAP	1.06265	0.765
42DAP/41DAP	0.87047	1
43DAP/42DAP	1.17194	0.823
47DAP/43DAP	1.4751	0.455
52DAP/47DAP	0.94544	0.806
57DAP/52DAP	0.99974	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79167	0.077
17DAP/reference	0.71737	0.018
27DAP/reference	0.86684	0.106
39DAP/reference	0.76119	0.046
41DAP/reference	0.64814	0.008
42DAP/reference	0.78628	0.009
43DAP/reference	0.85894	0.084
47DAP/reference	0.87706	0.042
52DAP/reference	1.24654	0.065
57DAP/reference	1.07318	0.239

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.51248	0.036
27DAP/17DAP	1.29444	0.476
39DAP/27DAP	0.99876	0.887
41DAP/39DAP	1.01582	1
42DAP/41DAP	0.8702	0.339
43DAP/42DAP	1.08459	0.585
47DAP/43DAP	0.85486	0.188
52DAP/47DAP	1.47533	0.338
57DAP/52DAP	1.22153	0.58
57DAP/7DAP	1.4601	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00619	0.758
17DAP/reference	1.11428	0.361
27DAP/reference	1.16165	0.03
39DAP/reference	0.8225	0.083
41DAP/reference	0.8123	0.044
42DAP/reference	0.7623	0.012
43DAP/reference	0.98162	0.48
47DAP/reference	0.84301	0.044
52DAP/reference	1.00533	0.74
57DAP/reference	1.09156	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75638	0.049
17DAP/reference	0.991	0.659
27DAP/reference	0.80452	0.051
39DAP/reference	0.87696	0.147
41DAP/reference	0.97782	0.481
42DAP/reference	0.79917	0.03
43DAP/reference	0.75671	0.058
47DAP/reference	0.75837	0.014
52DAP/reference	0.96813	0.433
57DAP/reference	0.74976	0.05

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1544	0.224
17DAP/reference	0.88423	0.255
27DAP/reference	1.18166	0.198
39DAP/reference	1.11594	0.227
41DAP/reference	1.07209	0.486
42DAP/reference	1.09809	0.701
43DAP/reference	0.92008	0.294
47DAP/reference	0.84089	0.049
52DAP/reference	1.15952	1
57DAP/reference	1.0905	0.549

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09654	0.966
26DAP/20DAP	0.99352	1
34DAP/26DAP	1.8072	0.819
51DAP/34DAP	1.12755	0.869
52DAP/51DAP	1.23285	0.689
53DAP/52DAP	1.2218	0.902
55DAP/53DAP	0.98958	0.807
57DAP/55DAP	0.84744	0.351
62DAP/57DAP	0.98735	0.994
68DAP/62DAP	1.14899	0.977
68DAP/14DAP	2.17906	0.074

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.06439	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.46216	0.814
Immature Eggplant/Mature Eggplant	1.26549	0.074
Ripe Pepper/Ripe Tomato	0.23315	0.224
Mature Eggplant/Ripe Tomato	0.47921	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.68437
1-1-2/M82	0.52774	1
12-2/M82	1.08169
12-4/M82	0.84188
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	0.91895
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.21359
5-3/M82	1.00913
6-2/M82	N/A	N/A
6-3/M82	1.27432
7-1/M82	1.07276
7-2/M82	1.01105
9-3-2/M82	N/A	N/A

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	1.0146	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92546	1
DC3000/delta hrp 6h	0.98039	0.95
DC3000/delta hrp 12h	1.04387	1
DC3000/delta hrp 24h	0.75116	0.077

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	3.36982	0.049
DC3000 delta B/DC3000 delta AB	1.13556	0.406

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.74417	1
Exp 36h	1.4478	1
Exp 60h	1.4143	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05562	1
Var 0h	0.91886	0.933
Var 12h I row2-row1	1.09589	0.613
Var 12h NI row2-row1	2.30777	1
Var 36h I row2-row1	1.13638	0.908
Var 36h NI row2-row1	0.47538	0.382
Var 60h I row2-row1	1.19398	1
Var 60h NI row2-row1	0.78079	0.932
Time course 0hI-0hNI	1.06641	0.988
Time course 12hI-12hNI	1.01799	0.876
Time course 36hI-36hNI	1.03874	0.722
Time course 60hI-60hNI	1.09355	0.673

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)	1.0218	0.798
transgenic ySAMdc/azygous control (breaker)	0.8986	0.251
transgenic ySAMdc/azygous control (red)	0.75372	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03483	0.587

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.8621	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.00964	1
Manapal/WT (break)	1.03584	1
Manapal/WT (red)	1.12313	1