Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.11.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09594	0.615
27DAP/17DAP	1.06794	0.868
39DAP/27DAP	0.82676	0.507
41DAP/39DAP	1.26228	0.25
42DAP/41DAP	0.85693	1
43DAP/42DAP	1.05726	1
47DAP/43DAP	0.89467	0.68
52DAP/47DAP	0.93201	0.799
57DAP/52DAP	1.10412	0.878

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87817	0.149
17DAP/reference	1.03107	0.27
27DAP/reference	0.98766	0.741
39DAP/reference	1.1824	0.504
41DAP/reference	0.98332	0.814
42DAP/reference	0.88641	0.019
43DAP/reference	0.98843	0.805
47DAP/reference	0.89377	0.006
52DAP/reference	0.7889	0.099
57DAP/reference	0.98445	0.61

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0559	0.708
27DAP/17DAP	0.9651	0.614
39DAP/27DAP	0.95718	0.556
41DAP/39DAP	0.90592	0.599
42DAP/41DAP	0.94018	0.649
43DAP/42DAP	1.05611	0.351
47DAP/43DAP	1.028	0.88
52DAP/47DAP	N/A	N/A
57DAP/52DAP	0.94656
57DAP/7DAP	1.12932

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3446	0.213
17DAP/reference	1.30827	0.092
27DAP/reference	1.18031	0.02
39DAP/reference	1.78478	0.006
41DAP/reference	1.74527	0.013
42DAP/reference	1.75616	0.007
43DAP/reference	1.991	0.007
47DAP/reference	1.38899	0.595
52DAP/reference	1.55307	0.016
57DAP/reference	1.54904	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95257	0.441
17DAP/reference	0.91968	0.153
27DAP/reference	0.85416	0.079
39DAP/reference	0.94072	0.25
41DAP/reference	0.88493	0.141
42DAP/reference	0.92883	0.261
43DAP/reference	0.84035	0.132
47DAP/reference	0.99939	0.77
52DAP/reference	0.98424	0.469
57DAP/reference	0.98128	0.549

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04527	0.723
17DAP/reference	1.02704	0.887
27DAP/reference	1.32715	0.027
39DAP/reference	1.33055	0.011
41DAP/reference	1.12493	0.286
42DAP/reference	1.12742	0.416
43DAP/reference	1.07342	0.88
47DAP/reference	0.95075	0.335
52DAP/reference	1.27696	0.167
57DAP/reference	0.95835	0.402

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98092	1
26DAP/20DAP	0.9418	1
34DAP/26DAP	1.06374	0.819
51DAP/34DAP	1.07649	0.445
52DAP/51DAP	1.12414	0.367
53DAP/52DAP	0.94865	0.811
55DAP/53DAP	1.09779	0.562
57DAP/55DAP	1.28124	0.348
62DAP/57DAP	0.91564	0.681
68DAP/62DAP	1.13462	0.919
68DAP/14DAP	1.06897	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.90265	0.175

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.50631
Mature Green Tomato/Ripe Tomato	1.62137
Immature Eggplant/Mature Eggplant	4.85348	0.05
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	76.5203	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06174	1
1-1-2/M82	0.99989	1
12-2/M82	1.0953	1
12-4/M82	0.9614	1
1-3/M82	0.94941	0.501
2-1-1/M82	1.04204	0.689
2-1/M82	1.16354	1
2-6/M82	0.99389	1
3-2/M82	0.92204	1
4-1-1/M82	0.98859	1
4-1/M82	0.90854	1
4-3-2/M82	1.04525	1
4-3/M82	0.9131	1
5-3/M82	0.96758	1
6-2/M82	1.10827	1
6-3/M82	0.9964	1
7-1/M82	1.01216	1
7-2/M82	0.96601	0.578
9-3-2/M82	0.78275	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.51275	0.254
IL2-6/WTpooled	0.90797	1
IL7-5/WTpooled	1.3587	0.635
IL7-3/WTpooled	1.17423	1
IL12-4/WTpooled	1.20945	0.673
IL1-4/WTpooled	1.2052	0.426
WT/WTpooled	1.01165	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98374	1
DC3000/delta hrp 6h	1.60226	1
DC3000/delta hrp 12h	0.85039	1
DC3000/delta hrp 24h	1.10689	0.322

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.99856	1
DC3000 delta B/DC3000 delta AB	1.04969	0.55

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	0.97959	1
Var 0h	0.93864	0.226
Var 12h I row2-row1	1.02213	0.736
Var 12h NI row2-row1	0.85598	0.494
Var 36h I row2-row1	1.35107	1
Var 36h NI row2-row1	1.09082	1
Var 60h I row2-row1	1.07966	1
Var 60h NI row2-row1	1.21838	0.904
Time course 0hI-0hNI	1.09525	0.852
Time course 12hI-12hNI	0.99059	0.978
Time course 36hI-36hNI	0.93645	0.255
Time course 60hI-60hNI	1.10036	0.254

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)	18.2372	0.272
transgenic ySAMdc/azygous control (breaker)	1.99513	1
transgenic ySAMdc/azygous control (red)	1.28964	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98041	0.186

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.10971	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.10889	1
Manapal/WT (break)	0.70236	0.299
Manapal/WT (red)	1.06386	0.413