Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.16.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04554	0.77
27DAP/17DAP	1.00957	1
39DAP/27DAP	0.72083	0.346
41DAP/39DAP	1.30211	0.323
42DAP/41DAP	1.01789	1
43DAP/42DAP	0.93464	0.846
47DAP/43DAP	1.15862	0.42
52DAP/47DAP	0.79077	0.466
57DAP/52DAP	0.9881	0.982

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00494	1
17DAP/reference	0.9583	0.448
27DAP/reference	0.99311	0.779
39DAP/reference	1.00742	0.722
41DAP/reference	1.05442	0.516
42DAP/reference	0.99376	0.531
43DAP/reference	0.96655	0.41
47DAP/reference	0.95776	0.077
52DAP/reference	0.96609	0.489
57DAP/reference	0.93208	0.147

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86459	0.093
27DAP/17DAP	1.0329	0.885
39DAP/27DAP	1.03166	0.698
41DAP/39DAP	0.99042	1
42DAP/41DAP	1.0672	0.615
43DAP/42DAP	1.05632	0.273
47DAP/43DAP	1.03339	0.837
52DAP/47DAP	0.97345	0.876
57DAP/52DAP	0.99695	0.887
57DAP/7DAP	1.02473	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98337	0.326
17DAP/reference	0.93717	0.018
27DAP/reference	0.97772	0.348
39DAP/reference	1.00031	1
41DAP/reference	0.96228	0.139
42DAP/reference	0.95578	0.058
43DAP/reference	0.97084	0.292
47DAP/reference	0.91881	0.128
52DAP/reference	0.99432	0.679
57DAP/reference	0.91613	0.019

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97558	0.503
17DAP/reference	1.04314	0.584
27DAP/reference	0.92086	0.15
39DAP/reference	0.88546	0.156
41DAP/reference	0.92981	0.315
42DAP/reference	0.86616	0.017
43DAP/reference	1.00299	0.875
47DAP/reference	0.89148	0.013
52DAP/reference	0.9452	0.066
57DAP/reference	1.00197	0.916

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97805	0.249
17DAP/reference	0.95476	0.381
27DAP/reference	1.02956	0.552
39DAP/reference	0.96477	0.05
41DAP/reference	1.01184	0.796
42DAP/reference	0.91486	0.028
43DAP/reference	0.96393	0.365
47DAP/reference	0.96558	0.348
52DAP/reference	0.92859	0.166
57DAP/reference	0.7693	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95144	1
26DAP/20DAP	0.95272	1
34DAP/26DAP	0.99929	1
51DAP/34DAP	0.96559	0.758
52DAP/51DAP	1.0518	0.616
53DAP/52DAP	0.98481	0.96
55DAP/53DAP	1.08648	0.893
57DAP/55DAP	0.80942	0.464
62DAP/57DAP	1.02276	0.994
68DAP/62DAP	1.13986	0.747
68DAP/14DAP	1.09624	0.694

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.95212	0.253

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.93226	0.591
Mature Green Tomato/Ripe Tomato	0.83225	0.317
Immature Eggplant/Mature Eggplant	1.03795	0.507
Ripe Pepper/Ripe Tomato	1.14435	1
Mature Eggplant/Ripe Tomato	1.65833	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01811	1
1-1-2/M82	0.84379	0.958
12-2/M82	1.05892	1
12-4/M82	0.96827	1
1-3/M82	0.92748	0.378
2-1-1/M82	1.16048	0.332
2-1/M82	1.00241
2-6/M82	1.04268	1
3-2/M82	0.91695
4-1-1/M82	0.95753	1
4-1/M82	0.79967	1
4-3-2/M82	0.81817	0.698
4-3/M82	1.17064
5-3/M82	0.9909	1
6-2/M82	0.99971	1
6-3/M82	0.97228	1
7-1/M82	N/A	N/A
7-2/M82	0.92335	0.881
9-3-2/M82	0.82823	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.00613	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.98177	1
IL12-4/WTpooled	1.00181	1
IL1-4/WTpooled	0.88117
WT/WTpooled	1.00299	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	1.03126	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05457	0.846
DC3000/delta hrp 6h	0.98599	0.95
DC3000/delta hrp 12h	0.90505	1
DC3000/delta hrp 24h	0.95011	0.67

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.09019	0.087
DC3000 delta B/DC3000 delta AB	1.03105	0.677

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89902	1
Exp 36h	0.74935	0.539
Exp 60h	0.94634	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01939	1
Var 0h	0.8635	0.933
Var 12h I row2-row1	1.02689	0.736
Var 12h NI row2-row1	0.87613	0.627
Var 36h I row2-row1	0.88825	0.805
Var 36h NI row2-row1	0.94154	0.645
Var 60h I row2-row1	1.39082	0.562
Var 60h NI row2-row1	1.16882	0.904
Time course 0hI-0hNI	1.09384	0.764
Time course 12hI-12hNI	1.00975	0.892
Time course 36hI-36hNI	0.94044	0.19
Time course 60hI-60hNI	0.99943	1

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)	1.00173	1
transgenic ySAMdc/azygous control (breaker)	0.8123	0.15
transgenic ySAMdc/azygous control (red)	0.92013	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01348	0.35

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.29049	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.9773	1
Manapal/WT (break)	0.89497	1
Manapal/WT (red)	1.23145	0.222