Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.16.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14213	0.739
27DAP/17DAP	1.16807	0.859
39DAP/27DAP	1.19363	0.735
41DAP/39DAP	0.89144	0.54
42DAP/41DAP	0.99005	1
43DAP/42DAP	1.14656	1
47DAP/43DAP	1.36977	0.746
52DAP/47DAP	1.36719	0.757
57DAP/52DAP	1.11445	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00654	1
17DAP/reference	1.03014	0.127
27DAP/reference	0.99207	0.797
39DAP/reference	0.99164	0.885
41DAP/reference	1.05254	0.079
42DAP/reference	0.97421	0.218
43DAP/reference	0.99457	0.861
47DAP/reference	1.01196	0.817
52DAP/reference	1.09436	0.092
57DAP/reference	1.02459	0.927

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99872	0.899
27DAP/17DAP	0.99289	0.919
39DAP/27DAP	1.05483	0.532
41DAP/39DAP	1.0394	0.774
42DAP/41DAP	0.96574	0.662
43DAP/42DAP	1.0136	0.478
47DAP/43DAP	0.98754	0.928
52DAP/47DAP	0.98635	0.919
57DAP/52DAP	1.00263	1
57DAP/7DAP	1.01686	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94951	0.361
17DAP/reference	0.93342	0.082
27DAP/reference	0.8897	0.026
39DAP/reference	0.93441	0.064
41DAP/reference	1.00465	1
42DAP/reference	0.95468	0.16
43DAP/reference	0.9141	0.054
47DAP/reference	0.94129	0.079
52DAP/reference	0.92416	0.012
57DAP/reference	1.00679	0.804

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91587	0.296
17DAP/reference	1.022	0.613
27DAP/reference	0.92226	0.24
39DAP/reference	0.94425	0.202
41DAP/reference	1.01993	0.749
42DAP/reference	0.99147	0.594
43DAP/reference	0.96196	0.459
47DAP/reference	1.04911	0.212
52DAP/reference	0.97497	0.28
57DAP/reference	0.97651	0.549

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98753	0.566
17DAP/reference	0.9581	0.358
27DAP/reference	0.95615	0.062
39DAP/reference	0.92366	0.023
41DAP/reference	1.01719	0.754
42DAP/reference	0.92269	0.134
43DAP/reference	0.94105	0.038
47DAP/reference	0.98569	0.574
52DAP/reference	0.97578	0.704
57DAP/reference	1.04298	0.481

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99937	1
26DAP/20DAP	0.99845	1
34DAP/26DAP	1.02467	1
51DAP/34DAP	1.0454	0.677
52DAP/51DAP	0.98129	1
53DAP/52DAP	1.04673	0.783
55DAP/53DAP	0.98708	0.864
57DAP/55DAP	1.06161	0.51
62DAP/57DAP	0.91663	0.871
68DAP/62DAP	0.87047	0.609
68DAP/14DAP	1.06565	0.504

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.96844	0.466

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.71841	0.132
Immature Eggplant/Mature Eggplant	1.3613	0.085
Ripe Pepper/Ripe Tomato	0.08552	0.224
Mature Eggplant/Ripe Tomato	0.04375	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02533	1
1-1-2/M82	1.02848	1
12-2/M82	0.89061	0.955
12-4/M82	1.05114	1
1-3/M82	1.03033	1
2-1-1/M82	0.9929	1
2-1/M82	1.61449	1
2-6/M82	0.93244	1
3-2/M82	0.95639	1
4-1-1/M82	1.0123	1
4-1/M82	1.06128	1
4-3-2/M82	1.07159	1
4-3/M82	0.97287	1
5-3/M82	1.03203	1
6-2/M82	1.05227	1
6-3/M82	1.00959	1
7-1/M82	1.13547
7-2/M82	0.99136	1
9-3-2/M82	1.02963	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.37301
IL12-4/WTpooled	0.90382
IL1-4/WTpooled	1.05374
WT/WTpooled	N/A	N/A

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	1.03039	0.921
DC3000/delta hrp 6h	1.13603	1
DC3000/delta hrp 12h	1.0433	1
DC3000/delta hrp 24h	1.01938	0.71

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.02643	0.476
DC3000 delta B/DC3000 delta AB	1.0692	0.443

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00018	1
Exp 36h	N/A	N/A
Exp 60h	1.2468	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99447	1
Var 0h	1.10428	0.98
Var 12h I row2-row1	1.10585	0.196
Var 12h NI row2-row1	1.06492	1
Var 36h I row2-row1	1.05625	1
Var 36h NI row2-row1	1.00473	1
Var 60h I row2-row1	1.14527	0.562
Var 60h NI row2-row1	0.93894	0.359
Time course 0hI-0hNI	1.05299	0.852
Time course 12hI-12hNI	1.0523	0.633
Time course 36hI-36hNI	0.96664	0.468
Time course 60hI-60hNI	1.08274	0.096

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)	0.85919	0.32
transgenic ySAMdc/azygous control (breaker)	1.29946	0.248
transgenic ySAMdc/azygous control (red)	1.05317	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98199	0.122

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.9219	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.04184	0.088
Manapal/WT (break)	1.17999	1
Manapal/WT (red)	1.86919	0.126