Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.10.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09483	0.755
27DAP/17DAP	1.00892	1
39DAP/27DAP	0.76164	0.27
41DAP/39DAP	1.25583	0.134
42DAP/41DAP	0.90651	1
43DAP/42DAP	0.89465	0.822
47DAP/43DAP	1.08684	0.595
52DAP/47DAP	1.32255	0.376
57DAP/52DAP	0.99505	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98503	0.601
17DAP/reference	0.97647	0.503
27DAP/reference	1.00177	1
39DAP/reference	1.03616	0.465
41DAP/reference	1.04773	0.421
42DAP/reference	0.98924	0.359
43DAP/reference	0.99902	0.942
47DAP/reference	0.95944	0.083
52DAP/reference	0.98809	0.546
57DAP/reference	0.9391	0.118

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05279	0.5
27DAP/17DAP	0.99161	0.887
39DAP/27DAP	0.94143	0.52
41DAP/39DAP	1.05147	0.79
42DAP/41DAP	1.06168	0.582
43DAP/42DAP	0.9312	0.079
47DAP/43DAP	0.99706	0.997
52DAP/47DAP	1.0241	0.919
57DAP/52DAP	1.0197	0.899
57DAP/7DAP	1.07073	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97817
17DAP/reference	1.00018	1
27DAP/reference	0.97688	0.43
39DAP/reference	0.99525
41DAP/reference	0.91905	0.009
42DAP/reference	1.0194	0.686
43DAP/reference	0.9614	0.368
47DAP/reference	0.96174	0.293
52DAP/reference	0.91745	0.017
57DAP/reference	0.9711	0.27

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06138	0.456
17DAP/reference	1.04532	0.367
27DAP/reference	1.02374	0.875
39DAP/reference	0.9805	0.359
41DAP/reference	1.0005	0.735
42DAP/reference	1.01964	0.794
43DAP/reference	1.08023	0.173
47DAP/reference	0.99965	0.812
52DAP/reference	0.96255	0.051
57DAP/reference	1.01718	0.887

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04039	0.469
17DAP/reference	1.01145	0.842
27DAP/reference	1.00364	1
39DAP/reference	1.00336	1
41DAP/reference	0.99217	0.682
42DAP/reference	0.99601	1
43DAP/reference	0.93968	0.125
47DAP/reference	0.94977	0.191
52DAP/reference	0.9121	0.211
57DAP/reference	0.813	0.03

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93642	0.246
26DAP/20DAP	0.98645	1
34DAP/26DAP	0.86424	0.247
51DAP/34DAP	0.99289	0.946
52DAP/51DAP	1.0697	0.377
53DAP/52DAP	1.02196	0.901
55DAP/53DAP	0.96662	0.746
57DAP/55DAP	0.9689	0.854
62DAP/57DAP	0.97885	0.994
68DAP/62DAP	0.89726	0.378
68DAP/14DAP	1.20561	0.521

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.93309	0.269

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	6.89654	0.113
Mature Green Tomato/Ripe Tomato	1.1019	1
Immature Eggplant/Mature Eggplant	4.09596	0.043
Ripe Pepper/Ripe Tomato	1.33969	1
Mature Eggplant/Ripe Tomato	16.813	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.93232	0.605
1-1-2/M82	0.99577	1
12-2/M82	0.94726	0.955
12-4/M82	0.99767	1
1-3/M82	1.05539	1
2-1-1/M82	0.98589	1
2-1/M82	1.20285
2-6/M82	0.98866	1
3-2/M82	0.99413	1
4-1-1/M82	0.92326	1
4-1/M82	0.9331
4-3-2/M82	0.8969	0.698
4-3/M82	0.97793	1
5-3/M82	0.94699	1
6-2/M82	1.02027	1
6-3/M82	0.99677	1
7-1/M82	0.94257	0.443
7-2/M82	1.00838	1
9-3-2/M82	0.80357	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.05902
IL2-6/WTpooled	1.04545	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.02497	1
IL12-4/WTpooled	0.95238	1
IL1-4/WTpooled	1.09962	1
WT/WTpooled	0.98998	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	1.23602	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07961	0.692
DC3000/delta hrp 6h	0.96286	0.95
DC3000/delta hrp 12h	0.94842	1
DC3000/delta hrp 24h	0.98661	0.957

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.97485	0.803
DC3000 delta B/DC3000 delta AB	1.03012	0.565

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9396	1
Exp 36h	0.65299	0.449
Exp 60h	0.68308	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98788	1
Var 0h	10.039	0.936
Var 12h I row2-row1	1.11991	0.272
Var 12h NI row2-row1	1.01813	1
Var 36h I row2-row1	0.83862	1
Var 36h NI row2-row1	0.97822	0.791
Var 60h I row2-row1	1.26891	0.562
Var 60h NI row2-row1	0.92795	0.932
Time course 0hI-0hNI	1.03364	0.852
Time course 12hI-12hNI	0.99095	0.984
Time course 36hI-36hNI	0.90668	0.22
Time course 60hI-60hNI	1.03686	0.575

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)	1.95005	0.541
transgenic ySAMdc/azygous control (breaker)	1.07156	1
transgenic ySAMdc/azygous control (red)	1.33673	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00508	0.766

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.93552	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.33994	1
Manapal/WT (break)	1.19614	0.381
Manapal/WT (red)	1.39149	1