Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.16.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.73432	0.073
27DAP/17DAP	0.97972	0.947
39DAP/27DAP	0.96456	0.7
41DAP/39DAP	1.10942	0.921
42DAP/41DAP	1.07939	1
43DAP/42DAP	0.83198	0.556
47DAP/43DAP	1.08022	0.999
52DAP/47DAP	1.56867	0.371
57DAP/52DAP	0.749	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91395	0.352
17DAP/reference	0.93681	0.224
27DAP/reference	0.95514	0.428
39DAP/reference	0.9727	0.611
41DAP/reference	0.90308	0.085
42DAP/reference	0.88445	0.006
43DAP/reference	0.97088	0.611
47DAP/reference	0.92537	0.055
52DAP/reference	0.75334	0.077
57DAP/reference	0.9197	0.096

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88407	0.402
27DAP/17DAP	0.91094	0.684
39DAP/27DAP	1.01728	0.811
41DAP/39DAP	1.015	1
42DAP/41DAP	1.0254	0.924
43DAP/42DAP	1.1034	0.351
47DAP/43DAP	1.00655	0.989
52DAP/47DAP	0.97257	0.902
57DAP/52DAP	0.86172	0.339
57DAP/7DAP	0.5572	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89273	0.066
17DAP/reference	0.91189	0.22
27DAP/reference	1.02889	0.974
39DAP/reference	1.05484	0.46
41DAP/reference	1.03001	0.891
42DAP/reference	1.03417	1
43DAP/reference	1.09299	0.364
47DAP/reference	0.82531	0.079
52DAP/reference	1.06018	0.563
57DAP/reference	1.16102	0.268

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91632	0.362
17DAP/reference	0.88683	0.03
27DAP/reference	0.86304	0.041
39DAP/reference	0.81772	0.012
41DAP/reference	0.96115	0.412
42DAP/reference	0.97326	0.482
43DAP/reference	0.91901	0.212
47DAP/reference	0.93824	0.168
52DAP/reference	0.88165	0.006
57DAP/reference	0.91044	0.063

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89499	0.197
17DAP/reference	0.82212	0.07
27DAP/reference	0.87887	0.113
39DAP/reference	0.89378	0.111
41DAP/reference	0.85132	0.058
42DAP/reference	1.13706	0.627
43DAP/reference	1.13248	0.803
47DAP/reference	0.89273	0.049
52DAP/reference	0.87332	0.167
57DAP/reference	0.97584	0.602

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.89566	0.773
26DAP/20DAP	0.97092	1
34DAP/26DAP	0.96759	0.961
51DAP/34DAP	0.93633	0.579
52DAP/51DAP	1.09461	0.638
53DAP/52DAP	0.95628	0.767
55DAP/53DAP	1.08833	0.689
57DAP/55DAP	0.96881	0.804
62DAP/57DAP	0.94894	0.871
68DAP/62DAP	0.82428	0.152
68DAP/14DAP	1.08869	0.785

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.82656	0.224

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.29538	0.058
Mature Green Tomato/Ripe Tomato	1.09348	1
Immature Eggplant/Mature Eggplant	1.36268	0.096
Ripe Pepper/Ripe Tomato	0.73966	0.224
Mature Eggplant/Ripe Tomato	1.09196	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04054	1
1-1-2/M82	0.81897	0.958
12-2/M82	1.05952	1
12-4/M82	1.08629	1
1-3/M82	0.84394	0.441
2-1-1/M82	1.12682	0.457
2-1/M82	N/A	N/A
2-6/M82	1.01926	1
3-2/M82	1.02651
4-1-1/M82	0.78844
4-1/M82	1.26491
4-3-2/M82	0.81751	0.487
4-3/M82	0.91045
5-3/M82	0.99895	1
6-2/M82	0.89663	1
6-3/M82	0.93211	1
7-1/M82	1.07082
7-2/M82	0.91135	0.599
9-3-2/M82	0.73612	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.76649	0.247
IL2-6/WTpooled	1.2679	0.419
IL7-5/WTpooled	0.73319	0.559
IL7-3/WTpooled	0.74231	0.298
IL12-4/WTpooled	0.90301	0.71
IL1-4/WTpooled	0.91108	0.699
WT/WTpooled	0.98273	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	0.86176	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00739	1
DC3000/delta hrp 6h	1.00591	0.95
DC3000/delta hrp 12h	0.81008	1
DC3000/delta hrp 24h	2.41453	0.032

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.41471	0.081
DC3000 delta B/DC3000 delta AB	1.14129	0.336

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.24563	1
Exp 36h	1.07267	1
Exp 60h	1.01713	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02548	1
Var 0h	0.8371	1
Var 12h I row2-row1	0.99227	1
Var 12h NI row2-row1	1.03072	1
Var 36h I row2-row1	1.10518	0.291
Var 36h NI row2-row1	1.05333	1
Var 60h I row2-row1	1.36641	0.562
Var 60h NI row2-row1	0.98418	1
Time course 0hI-0hNI	1.17139	0.377
Time course 12hI-12hNI	0.87446	0.108
Time course 36hI-36hNI	0.91598	0.114
Time course 60hI-60hNI	0.93949	0.319

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)	0.81437	0.301
transgenic ySAMdc/azygous control (breaker)	0.93212	1
transgenic ySAMdc/azygous control (red)	0.99257	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03116	0.13

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.08514	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.84147	0.172
Manapal/WT (break)	0.71213	0.299
Manapal/WT (red)	1.1522	0.413