Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.11.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9753	0.779
27DAP/17DAP	1.20815	0.801
39DAP/27DAP	0.77485	0.414
41DAP/39DAP	1.17837	0.225
42DAP/41DAP	1.08008	1
43DAP/42DAP	1.1153	1
47DAP/43DAP	1.23082	0.563
52DAP/47DAP	1.34571	0.506
57DAP/52DAP	1.14863	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12461	0.46
17DAP/reference	1.12771	0.143
27DAP/reference	0.95949	0.581
39DAP/reference	1.02579	0.857
41DAP/reference	1.09348	0.365
42DAP/reference	0.8034	0.001
43DAP/reference	1.01476	0.957
47DAP/reference	0.89954	0.025
52DAP/reference	0.82661	0.093
57DAP/reference	0.82316	0.03

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90338	0.376
27DAP/17DAP	0.98768	0.919
39DAP/27DAP	0.9822	0.887
41DAP/39DAP	1.171	0.807
42DAP/41DAP	0.96191	0.687
43DAP/42DAP	1.13286	0.413
47DAP/43DAP	0.97295	0.877
52DAP/47DAP	1.05251	0.804
57DAP/52DAP	0.95941	0.695
57DAP/7DAP	1.14062	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88825	0.203
17DAP/reference	0.95835	0.389
27DAP/reference	0.91779	0.185
39DAP/reference	0.69474	0.017
41DAP/reference	0.60077	0.009
42DAP/reference	0.80079	0.073
43DAP/reference	0.70293	0.02
47DAP/reference	0.85447	0.222
52DAP/reference	0.74703	0.077
57DAP/reference	0.90255	0.183

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20498	0.36
17DAP/reference	0.91068	0.245
27DAP/reference	0.97503	0.483
39DAP/reference	0.80421	0.056
41DAP/reference	0.70359	0.059
42DAP/reference	0.87659	0.121
43DAP/reference	1.09948	0.719
47DAP/reference	0.83198	0.023
52DAP/reference	0.90476	0.111
57DAP/reference	1.04595	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03853	0.74
17DAP/reference	0.94265	0.519
27DAP/reference	1.00311	0.763
39DAP/reference	0.95261	0.36
41DAP/reference	0.97923	0.618
42DAP/reference	0.89106	0.22
43DAP/reference	0.85382	0.171
47DAP/reference	0.83723	0.174
52DAP/reference	1.04511	1
57DAP/reference	0.70871	0.033

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04309	1
26DAP/20DAP	0.77874	0.317
34DAP/26DAP	1.00286	1
51DAP/34DAP	0.83948	0.311
52DAP/51DAP	0.95144	1
53DAP/52DAP	0.87037	0.379
55DAP/53DAP	1.17286	0.656
57DAP/55DAP	0.77876	0.149
62DAP/57DAP	1.04831	1
68DAP/62DAP	1.79683	0.155
68DAP/14DAP	2.71343	0.558

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.89395	0.129

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.73678	0.182
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.18155
12-2/M82	N/A	N/A
12-4/M82	0.61687
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	1.10112
4-1-1/M82	N/A	N/A
4-1/M82	0.09441
4-3-2/M82	0.73577	0.698
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.92318
7-2/M82	N/A	N/A
9-3-2/M82	0.87556	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.98839
IL2-6/WTpooled	1.14924	0.584
IL7-5/WTpooled	0.94633	1
IL7-3/WTpooled	0.88079	0.418
IL12-4/WTpooled	1.05462	0.532
IL1-4/WTpooled	0.97824	0.834
WT/WTpooled	0.96917	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	1.13855	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.12952	0.724
DC3000/delta hrp 6h	1.49911	1
DC3000/delta hrp 12h	1.13383
DC3000/delta hrp 24h	2.13423	0.025

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.20093
DC3000 delta B/DC3000 delta AB	0.99466	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
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	0.99951	1
Var 0h	0.97409	1
Var 12h I row2-row1	1.08182	0.736
Var 12h NI row2-row1	0.90431	0.466
Var 36h I row2-row1	1.12658	1
Var 36h NI row2-row1	0.575	0.225
Var 60h I row2-row1	1.092	0.562
Var 60h NI row2-row1	1.3272	0.904
Time course 0hI-0hNI	1.01365	1
Time course 12hI-12hNI	0.96477	0.831
Time course 36hI-36hNI	0.79121	0.076
Time course 60hI-60hNI	3.39827	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)	4.64609	0.261
transgenic ySAMdc/azygous control (breaker)	0.85735	0.49
transgenic ySAMdc/azygous control (red)	1.28072	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93714	0.085

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.66003	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	2.45657	0.183
Manapal/WT (red)	N/A	N/A