Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.17.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07147	0.975
27DAP/17DAP	0.88612	0.73
39DAP/27DAP	1.00582	1
41DAP/39DAP	0.78589	0.387
42DAP/41DAP	1.20838	0.856
43DAP/42DAP	1.35992	0.313
47DAP/43DAP	1.01224	0.92
52DAP/47DAP	0.88211	0.677
57DAP/52DAP	1.13379	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22415	0.278
17DAP/reference	0.88106	0.536
27DAP/reference	0.97371	0.763
39DAP/reference	1.2307	0.393
41DAP/reference	1.06397	0.516
42DAP/reference	1.00824	0.645
43DAP/reference	1.0065	0.924
47DAP/reference	1.27928	0.015
52DAP/reference	1.0333	0.951
57DAP/reference	0.90436	0.056

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.43343	0.036
27DAP/17DAP	0.9244	0.684
39DAP/27DAP	0.59699	0.032
41DAP/39DAP	1.09853	0.748
42DAP/41DAP	0.99422	0.83
43DAP/42DAP	0.83235	0.116
47DAP/43DAP	0.99727	0.947
52DAP/47DAP	1.07092	0.826
57DAP/52DAP	1.21545	0.686
57DAP/7DAP	1.03252	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.44208	0.031
17DAP/reference	0.9897	0.599
27DAP/reference	0.93736	0.325
39DAP/reference	0.69335	0.011
41DAP/reference	0.61632	0.012
42DAP/reference	0.71983	0.09
43DAP/reference	0.93252	0.279
47DAP/reference	1.01151	1
52DAP/reference	0.7741	0.02
57DAP/reference	0.96099	0.353

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8467	0.182
17DAP/reference	0.87173	0.326
27DAP/reference	0.91105	0.212
39DAP/reference	1.0076	0.642
41DAP/reference	1.00482	0.702
42DAP/reference	0.95554	0.321
43DAP/reference	1.19058	0.91
47DAP/reference	1.19015	0.153
52DAP/reference	1.00869	0.761
57DAP/reference	1.13285	0.581

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.57932	0.28
17DAP/reference	1.10752	0.814
27DAP/reference	1.33524	0.034
39DAP/reference	1.29893	0.029
41DAP/reference	1.05096	0.777
42DAP/reference	1.06664	0.716
43DAP/reference	1.15738	0.275
47DAP/reference	0.82487	0.12
52DAP/reference	1.22092	0.262
57DAP/reference	1.07333	0.909

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91859
26DAP/20DAP	1.14429	0.598
34DAP/26DAP	1.16491	0.819
51DAP/34DAP	1.33706	0.066
52DAP/51DAP	1.03595	0.836
53DAP/52DAP	0.74465	0.06
55DAP/53DAP	0.56415	0.019
57DAP/55DAP	0.90369	0.629
62DAP/57DAP	1.00681	1
68DAP/62DAP	1.16331	0.899
68DAP/14DAP	1.17822	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.28664	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	4.09926	0.015
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	7.09718
Mature Eggplant/Ripe Tomato	4.77649	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.9694	1
12-2/M82	N/A	N/A
12-4/M82	0.77466	1
1-3/M82	N/A	N/A
2-1-1/M82	0.41227
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	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.77757
5-3/M82	0.67383	1
6-2/M82	N/A	N/A
6-3/M82	0.84912
7-1/M82	0.72007
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.05994	0.46
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.77787	0.31
IL12-4/WTpooled	0.91979	0.71
IL1-4/WTpooled	1.12637	1
WT/WTpooled	1.08653	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	0.83339	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95794	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.26002	1
DC3000/delta hrp 24h	0.5038	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.66653	0.024
DC3000 delta B/DC3000 delta AB	0.62239	0.02

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	0.98609	1
Var 0h	1.24537	0.936
Var 12h I row2-row1	0.77336	0.338
Var 12h NI row2-row1	1.06876	1
Var 36h I row2-row1	1.0512	0.908
Var 36h NI row2-row1	1.37584	0.482
Var 60h I row2-row1	0.88102	0.582
Var 60h NI row2-row1	1.21171	0.904
Time course 0hI-0hNI	0.94378	0.615
Time course 12hI-12hNI	1.00456	1
Time course 36hI-36hNI	0.89127	0.097
Time course 60hI-60hNI	0.18651	0.005

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	0.22755	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.41507	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	4.88224	0.134