Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.13.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1292	0.656
27DAP/17DAP	1.03637	1
39DAP/27DAP	0.82722	0.425
41DAP/39DAP	1.59499	0.212
42DAP/41DAP	0.93677	1
43DAP/42DAP	1.00785	1
47DAP/43DAP	1.04229	0.965
52DAP/47DAP	1.20153	0.545
57DAP/52DAP	1.03817	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03371	0.567
17DAP/reference	1.03408	0.528
27DAP/reference	0.99308	0.763
39DAP/reference	1.15692	0.403
41DAP/reference	1.02371	0.516
42DAP/reference	0.94081	0.012
43DAP/reference	1.02116	0.678
47DAP/reference	0.95931	0.055
52DAP/reference	0.98367	0.564
57DAP/reference	0.94177	0.101

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00841	0.975
27DAP/17DAP	0.9841	0.684
39DAP/27DAP	1.05424	0.519
41DAP/39DAP	1.04093	0.853
42DAP/41DAP	0.97855	0.776
43DAP/42DAP	0.9829	0.709
47DAP/43DAP	1.01479	0.93
52DAP/47DAP	0.99676	0.969
57DAP/52DAP	1.05894	0.695
57DAP/7DAP	1.00954	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8605	0.07
17DAP/reference	0.94015	0.028
27DAP/reference	1.01127	0.664
39DAP/reference	0.96862	0.146
41DAP/reference	0.94729	0.058
42DAP/reference	0.94621	0.058
43DAP/reference	0.96034	0.385
47DAP/reference	0.90123	0.101
52DAP/reference	0.95323	0.179
57DAP/reference	0.94184	0.118

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9791	0.639
17DAP/reference	0.98435	0.51
27DAP/reference	0.94212	0.269
39DAP/reference	0.92883	0.119
41DAP/reference	0.9175	0.115
42DAP/reference	0.96539	0.289
43DAP/reference	0.94546	0.236
47DAP/reference	1.02373	0.731
52DAP/reference	0.94341	0.131
57DAP/reference	1.00196	0.916

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99782	0.804
17DAP/reference	1.00551	0.988
27DAP/reference	1.0166	0.644
39DAP/reference	0.99155	0.591
41DAP/reference	0.98008	0.56
42DAP/reference	0.94881	0.108
43DAP/reference	0.98609	0.639
47DAP/reference	0.96541	0.465
52DAP/reference	0.98261	0.732
57DAP/reference	0.86132	0.042

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96356	1
26DAP/20DAP	0.95768	0.317
34DAP/26DAP	1.0361	1
51DAP/34DAP	0.96037	0.681
52DAP/51DAP	1.0312	0.704
53DAP/52DAP	1.00053	1
55DAP/53DAP	0.97251	0.725
57DAP/55DAP	1.1706	0.854
62DAP/57DAP	1.03498	0.868
68DAP/62DAP	0.96302	0.747
68DAP/14DAP	0.99309	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.95554	0.198

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.82927	0.028
Immature Eggplant/Mature Eggplant	1.69523	0.05
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01557	1
1-1-2/M82	0.99231	1
12-2/M82	0.91146	0.955
12-4/M82	0.97367	1
1-3/M82	0.86613	0.378
2-1-1/M82	1.0781	0.764
2-1/M82	0.97601
2-6/M82	0.90973	1
3-2/M82	0.91056	1
4-1-1/M82	1.03083	1
4-1/M82	0.75587	1
4-3-2/M82	0.93226	1
4-3/M82	1.01249	1
5-3/M82	1.00038	1
6-2/M82	1.00208	1
6-3/M82	1.04225	1
7-1/M82	1.00505
7-2/M82	0.96267	0.796
9-3-2/M82	0.75925	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.08292	0.493
IL2-6/WTpooled	0.89698	1
IL7-5/WTpooled	1.08864
IL7-3/WTpooled	0.90286	0.418
IL12-4/WTpooled	0.98156	1
IL1-4/WTpooled	1.04867	1
WT/WTpooled	1.00359	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	1.68374

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00855	0.921
DC3000/delta hrp 6h	0.82588	0.95
DC3000/delta hrp 12h	1.04251	1
DC3000/delta hrp 24h	0.97618	0.875

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.01377	0.648
DC3000 delta B/DC3000 delta AB	1.11407	0.311

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0392	1
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	0.9472	1
Var 0h	1.14747	0.782
Var 12h I row2-row1	1.13832	0.204
Var 12h NI row2-row1	0.93891	0.713
Var 36h I row2-row1	1.03543	1
Var 36h NI row2-row1	0.99195	0.852
Var 60h I row2-row1	1.19075	1
Var 60h NI row2-row1	1.05804	1
Time course 0hI-0hNI	1.13135	0.764
Time course 12hI-12hNI	1.10214	0.275
Time course 36hI-36hNI	1.19251	0.05
Time course 60hI-60hNI	1.22001	0.009

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)	1.5057	1
transgenic ySAMdc/azygous control (breaker)	1.5971	0.248
transgenic ySAMdc/azygous control (red)	1.27392	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95735	0.066

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.33578	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.05133	1
Manapal/WT (break)	0.92356	1
Manapal/WT (red)	0.61767	0.187