Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.15.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83591	0.297
27DAP/17DAP	0.86713	0.649
39DAP/27DAP	1.17423	0.729
41DAP/39DAP	0.98411	0.911
42DAP/41DAP	1.13828	0.886
43DAP/42DAP	0.93796	0.834
47DAP/43DAP	1.0732	0.689
52DAP/47DAP	1.02987	0.96
57DAP/52DAP	1.03791	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.50513	0.03
17DAP/reference	1.07954	0.248
27DAP/reference	1.14326	0.165
39DAP/reference	0.96618	0.541
41DAP/reference	1.17516	0.221
42DAP/reference	1.30811	0.004
43DAP/reference	0.92704	0.394
47DAP/reference	1.14048	0.142
52DAP/reference	1.27414	0.038
57DAP/reference	1.22902	0.136

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88046	0.26
27DAP/17DAP	1.05129	0.957
39DAP/27DAP	1.0145	0.799
41DAP/39DAP	1.09909	0.531
42DAP/41DAP	0.96653	0.721
43DAP/42DAP	0.97294	0.729
47DAP/43DAP	1.08694	0.756
52DAP/47DAP	0.94346	0.739
57DAP/52DAP	1.0187	0.978
57DAP/7DAP	1.16401	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00832	1
17DAP/reference	0.82776	0.014
27DAP/reference	0.81847	0.014
39DAP/reference	0.95985	0.198
41DAP/reference	0.96742	0.431
42DAP/reference	0.96619	0.393
43DAP/reference	0.89227	0.054
47DAP/reference	1.11473	0.761
52DAP/reference	0.88246	0.137
57DAP/reference	0.85026	0.019

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99553	0.786
17DAP/reference	1.3115	0.058
27DAP/reference	1.26068	0.037
39DAP/reference	1.28475	0.233
41DAP/reference	1.49094	0.018
42DAP/reference	1.39694	0.011
43DAP/reference	1.01891	0.721
47DAP/reference	1.15704	0.039
52DAP/reference	1.26025	0.085
57DAP/reference	1.24069	0.593

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94951	0.422
17DAP/reference	0.98802	0.696
27DAP/reference	1.11056	0.871
39DAP/reference	0.78249	0.017
41DAP/reference	0.89472	0.132
42DAP/reference	1.13466	0.994
43DAP/reference	1.25066	0.625
47DAP/reference	1.27196	0.089
52DAP/reference	0.72153	0.15
57DAP/reference	2.04765	0.033

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91238	1
26DAP/20DAP	1.21311	0.195
34DAP/26DAP	0.99966	1
51DAP/34DAP	0.8293	0.108
52DAP/51DAP	0.99753	1
53DAP/52DAP	0.97346	0.79
55DAP/53DAP	1.12304	0.737
57DAP/55DAP	1.00556	0.927
62DAP/57DAP	1.27753	0.257
68DAP/62DAP	0.96511	0.81
68DAP/14DAP	0.67234	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.0036	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.28449	0.064
Immature Eggplant/Mature Eggplant	N/A	N/A
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	N/A	N/A
1-1-2/M82	0.85967
12-2/M82	N/A	N/A
12-4/M82	0.73775
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.01231	1
4-3-2/M82	1.26717
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.85621	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.08048	0.584
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.85946	1
IL12-4/WTpooled	1.09414	0.891
IL1-4/WTpooled	1.06776	1
WT/WTpooled	1.08179	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	0.76841	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	1.11445
DC3000/delta hrp 12h	1.09894	1
DC3000/delta hrp 24h	N/A	N/A

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.09592	0.25
DC3000 delta B/DC3000 delta AB	1.0885	0.345

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	0.99526
Var 0h	0.86451	1
Var 12h I row2-row1	0.87838	0.418
Var 12h NI row2-row1	1.21851	1
Var 36h I row2-row1	1.14693	0.489
Var 36h NI row2-row1	1.14812	1
Var 60h I row2-row1	1.07779	1
Var 60h NI row2-row1	1.08715	0.691
Time course 0hI-0hNI	1.02229	0.867
Time course 12hI-12hNI	0.96594	0.701
Time course 36hI-36hNI	0.9691	0.484
Time course 60hI-60hNI	0.64105	0.006

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)	0.7682	0.362
transgenic ySAMdc/azygous control (breaker)	1.17825	1
transgenic ySAMdc/azygous control (red)	1.04518	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.87739	0.097

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.93089	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.99694	0.096
Manapal/WT (break)	1.48761	0.381
Manapal/WT (red)	1.01543	1