Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.13.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91136	0.413
27DAP/17DAP	0.97967	1
39DAP/27DAP	1.10314	0.75
41DAP/39DAP	0.9489	0.769
42DAP/41DAP	1.25831	0.752
43DAP/42DAP	1.03838	1
47DAP/43DAP	0.97929	0.859
52DAP/47DAP	0.93199	0.781
57DAP/52DAP	1.01285	0.988

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98699	0.679
17DAP/reference	0.85685	0.342
27DAP/reference	0.89105	0.022
39DAP/reference	0.9122	0.298
41DAP/reference	0.98698	0.814
42DAP/reference	1.07394	0.108
43DAP/reference	1.00687	1
47DAP/reference	1.0229	0.646
52DAP/reference	0.95109	0.449
57DAP/reference	0.99499	0.639

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05265	0.379
27DAP/17DAP	0.98093	0.878
39DAP/27DAP	0.98485	0.908
41DAP/39DAP	1.03989	0.773
42DAP/41DAP	1.00152	1
43DAP/42DAP	1.00422	0.83
47DAP/43DAP	0.99488	0.99
52DAP/47DAP	0.97214	0.807
57DAP/52DAP	1.00357	1
57DAP/7DAP	0.94619	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97119	0.402
17DAP/reference	0.98939	0.447
27DAP/reference	0.94169	0.035
39DAP/reference	0.94817	0.073
41DAP/reference	0.9336	0.064
42DAP/reference	0.87197	0.02
43DAP/reference	0.92099	0.03
47DAP/reference	0.91815	0.066
52DAP/reference	0.91098	0.023
57DAP/reference	0.89863	0.038

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02156	0.812
17DAP/reference	0.99644	0.766
27DAP/reference	0.95401	0.407
39DAP/reference	0.86588	0.165
41DAP/reference	0.85599	0.06
42DAP/reference	0.95424	0.289
43DAP/reference	0.91992	0.157
47DAP/reference	0.99926	0.79
52DAP/reference	0.87854	0.007
57DAP/reference	0.91491	0.019

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00572	1
17DAP/reference	0.97727	0.592
27DAP/reference	0.94586	0.102
39DAP/reference	0.95492	0.083
41DAP/reference	0.94603	0.132
42DAP/reference	0.9425	0.172
43DAP/reference	1.04493	0.515
47DAP/reference	0.85136	0.049
52DAP/reference	0.93451	0.327
57DAP/reference	0.9156	0.177

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02603	0.966
26DAP/20DAP	1.09458
34DAP/26DAP	0.96696	0.94
51DAP/34DAP	1.04095	0.706
52DAP/51DAP	1.0287	0.783
53DAP/52DAP	N/A	N/A
55DAP/53DAP	0.96285
57DAP/55DAP	1.10925	0.764
62DAP/57DAP	1.02545	0.902
68DAP/62DAP	1.04326	0.956
68DAP/14DAP	1.44449	0.041

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.11967	0.184

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.27835	0.176
Mature Green Tomato/Ripe Tomato	1.01658	0.835
Immature Eggplant/Mature Eggplant	1.15846	0.259
Ripe Pepper/Ripe Tomato	1.0342	1
Mature Eggplant/Ripe Tomato	1.36465	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04766	1
1-1-2/M82	0.91809	1
12-2/M82	0.98813	0.955
12-4/M82	1.12307	1
1-3/M82	0.93761	1
2-1-1/M82	0.76087	0.465
2-1/M82	1.10242	1
2-6/M82	0.9529	1
3-2/M82	0.90616	1
4-1-1/M82	0.99132	1
4-1/M82	0.8514	1
4-3-2/M82	0.82294	1
4-3/M82	0.90861	0.72
5-3/M82	0.99899	1
6-2/M82	0.99952	1
6-3/M82	1.05489	1
7-1/M82	1.01462	1
7-2/M82	0.93342	0.881
9-3-2/M82	0.79304	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.01632	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.0166	1
IL12-4/WTpooled	1.12337	0.624
IL1-4/WTpooled	1.08128
WT/WTpooled	1.00126	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	1.1267	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95322	1
DC3000/delta hrp 6h	1.19091	1
DC3000/delta hrp 12h	1.03361	1
DC3000/delta hrp 24h	1.07779	0.397

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.17457	0.076
DC3000 delta B/DC3000 delta AB	1.15166	0.261

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00422	1
Exp 36h	1.13742	1
Exp 60h	0.74774	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01746	1
Var 0h	1.17266	0.339
Var 12h I row2-row1	1.17975	0.224
Var 12h NI row2-row1	1.22753	1
Var 36h I row2-row1	1.19103	1
Var 36h NI row2-row1	1.08041	1
Var 60h I row2-row1	0.98457	0.832
Var 60h NI row2-row1	1.25603	0.904
Time course 0hI-0hNI	0.96487	0.829
Time course 12hI-12hNI	1.04946	0.786
Time course 36hI-36hNI	1.04157	0.881
Time course 60hI-60hNI	1.36171	0.025

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)	0.74692	0.267
transgenic ySAMdc/azygous control (breaker)	1.41006	1
transgenic ySAMdc/azygous control (red)	1.47027	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.91467	0.062

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.11988	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.77738	0.086
Manapal/WT (break)	1.68964	0.381
Manapal/WT (red)	0.91389	0.503