Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.18.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85782	0.427
27DAP/17DAP	1.18296	0.832
39DAP/27DAP	0.92903	0.631
41DAP/39DAP	1.09293	0.929
42DAP/41DAP	0.87589	1
43DAP/42DAP	1.12313	0.957
47DAP/43DAP	1.40462	0.196
52DAP/47DAP	1.11635	0.946
57DAP/52DAP	1.07041	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87995	0.046
17DAP/reference	0.9761	0.63
27DAP/reference	1.09985	0.216
39DAP/reference	0.98658	0.816
41DAP/reference	1.01815	1
42DAP/reference	0.91362	0.014
43DAP/reference	0.97052	0.576
47DAP/reference	1.05576	0.215
52DAP/reference	0.95321	0.341
57DAP/reference	0.94734	0.294

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9958	0.847
27DAP/17DAP	0.88669	0.684
39DAP/27DAP	1.04151	0.663
41DAP/39DAP	1.03197	0.801
42DAP/41DAP	1.00419	1
43DAP/42DAP	0.97422	0.618
47DAP/43DAP	1.01439	0.857
52DAP/47DAP	0.98597	0.917
57DAP/52DAP	1.02266	0.877
57DAP/7DAP	1.01935	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88369	0.122
17DAP/reference	0.82032	0.011
27DAP/reference	0.80295	0.012
39DAP/reference	0.93776	0.095
41DAP/reference	0.91264	0.058
42DAP/reference	0.85026	0.01
43DAP/reference	0.8689	0.066
47DAP/reference	1.01442	1
52DAP/reference	0.9166	0.137
57DAP/reference	0.94906	0.232

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93739	0.238
17DAP/reference	0.865	0.059
27DAP/reference	0.86028	0.203
39DAP/reference	0.90498	0.173
41DAP/reference	0.86571	0.058
42DAP/reference	0.74351	0.027
43DAP/reference	0.85642	0.121
47DAP/reference	0.94634	0.116
52DAP/reference	0.92883	0.093
57DAP/reference	0.97413	0.433

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84789	0.057
17DAP/reference	0.88659	0.189
27DAP/reference	0.87528	0.056
39DAP/reference	0.82892	0.021
41DAP/reference	0.83601	0.025
42DAP/reference	0.70698	0.019
43DAP/reference	0.79948	0.051
47DAP/reference	1.04291	0.562
52DAP/reference	0.74329	0.122
57DAP/reference	0.82552	0.054

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9611	1
26DAP/20DAP	1.02723	0.924
34DAP/26DAP	1.0857	0.819
51DAP/34DAP	0.94362	0.555
52DAP/51DAP	0.94706	1
53DAP/52DAP	1.02365	0.921
55DAP/53DAP	0.97652	0.735
57DAP/55DAP	1.04205	0.865
62DAP/57DAP	0.95125	0.871
68DAP/62DAP	1.14367	0.597
68DAP/14DAP	1.06893	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.86025	0.102

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.54328	0.115
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.39688	0.157
Ripe Pepper/Ripe Tomato	1.06061	1
Mature Eggplant/Ripe Tomato	0.88296	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00608	1
1-1-2/M82	1.04077	1
12-2/M82	1.0955	1
12-4/M82	1.0124	1
1-3/M82	0.88311	0.501
2-1-1/M82	1.16446	0.764
2-1/M82	1.46568	1
2-6/M82	1.03458	0.695
3-2/M82	0.89758
4-1-1/M82	0.96488	1
4-1/M82	0.94802
4-3-2/M82	0.95918
4-3/M82	1.11574	1
5-3/M82	0.93909	1
6-2/M82	0.98732	1
6-3/M82	0.99949	1
7-1/M82	0.98106	0.803
7-2/M82	1.10617	1
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	0.8625	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.49998	1
IL12-4/WTpooled	1.33629	0.52
IL1-4/WTpooled	0.91202
WT/WTpooled	1.10508	0.794

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	1.21455	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02845	0.894
DC3000/delta hrp 6h	1.05155	0.95
DC3000/delta hrp 12h	1.05976	1
DC3000/delta hrp 24h	1.09117	0.604

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.99367	1
DC3000 delta B/DC3000 delta AB	1.06578	0.491

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.14649	0.254
Exp 36h	1.49701	0.489
Exp 60h	1.3728	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0314	1
Var 0h	0.81399	0.594
Var 12h I row2-row1	0.93824	0.77
Var 12h NI row2-row1	1.06186	1
Var 36h I row2-row1	0.81439	1
Var 36h NI row2-row1	0.97224	0.791
Var 60h I row2-row1	0.75258	0.287
Var 60h NI row2-row1	0.95288	0.977
Time course 0hI-0hNI	1.01248	1
Time course 12hI-12hNI	1.05334	0.587
Time course 36hI-36hNI	1.31912	0.007
Time course 60hI-60hNI	3.42068	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)	0.84159	0.246
transgenic ySAMdc/azygous control (breaker)	0.64881	0.251
transgenic ySAMdc/azygous control (red)	0.88731	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00845	0.854

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.05599	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.35118	0.096
Manapal/WT (break)	1.40114	0.381
Manapal/WT (red)	0.85058	0.199