Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.16.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18202	0.281
27DAP/17DAP	1.2925	0.761
39DAP/27DAP	1.27279	0.615
41DAP/39DAP	1.10315	0.676
42DAP/41DAP	1.18497	0.681
43DAP/42DAP	0.90762	0.743
47DAP/43DAP	0.90881	0.705
52DAP/47DAP	1.19689	0.646
57DAP/52DAP	0.90937	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0002	1
17DAP/reference	1.0041	0.787
27DAP/reference	1.03558	0.468
39DAP/reference	1.03371	0.335
41DAP/reference	1.06714	0.221
42DAP/reference	1.04073	0.366
43DAP/reference	1.02995	0.287
47DAP/reference	1.00243	1
52DAP/reference	0.97845	0.546
57DAP/reference	1.02366	0.621

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.69561	0.099
27DAP/17DAP	1.06386	0.842
39DAP/27DAP	1.5248	0.054
41DAP/39DAP	2.31214	0.006
42DAP/41DAP	0.80863	0.019
43DAP/42DAP	0.79858	0.024
47DAP/43DAP	1.39155	0.012
52DAP/47DAP	0.76582	0.072
57DAP/52DAP	0.91353	0.484
57DAP/7DAP	1.19206	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92198	0.1
17DAP/reference	0.92351	0.013
27DAP/reference	0.98976	0.43
39DAP/reference	0.94819	0.012
41DAP/reference	0.97358	0.247
42DAP/reference	0.99986	0.828
43DAP/reference	0.94268	0.019
47DAP/reference	0.90561	0.101
52DAP/reference	0.90772	0.038
57DAP/reference	0.88173	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9684	0.58
17DAP/reference	1.02361	0.599
27DAP/reference	0.93835	0.257
39DAP/reference	1.01811	1
41DAP/reference	1.04642	0.878
42DAP/reference	0.92139	0.042
43DAP/reference	1.07745	0.373
47DAP/reference	0.9687	0.319
52DAP/reference	0.9683	0.28
57DAP/reference	0.96448	0.318

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90626	0.029
17DAP/reference	1.00371	1
27DAP/reference	0.98618	0.594
39DAP/reference	0.96622	0.058
41DAP/reference	1.01147	0.889
42DAP/reference	0.98211	0.671
43DAP/reference	0.92748	0.061
47DAP/reference	0.97596	0.478
52DAP/reference	0.92825	0.242
57DAP/reference	0.90381	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98641	1
26DAP/20DAP	0.86645	0.512
34DAP/26DAP	1.01915	1
51DAP/34DAP	0.91059	0.472
52DAP/51DAP	1.07038	0.522
53DAP/52DAP	1.11981	0.356
55DAP/53DAP	1.05205	0.703
57DAP/55DAP	1.0184	1
62DAP/57DAP	0.91854	0.871
68DAP/62DAP	0.92768	0.641
68DAP/14DAP	0.98832	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.11493	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.84759	0.343
Mature Green Tomato/Ripe Tomato	0.68074	0.086
Immature Eggplant/Mature Eggplant	1.38024	0.061
Ripe Pepper/Ripe Tomato	0.98053	1
Mature Eggplant/Ripe Tomato	0.39743	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95939	0.934
1-1-2/M82	1.08126	1
12-2/M82	1.08495	1
12-4/M82	1.01969	1
1-3/M82	0.99006	1
2-1-1/M82	0.83733	0.92
2-1/M82	1.12095	0.32
2-6/M82	1.02832	1
3-2/M82	0.91606
4-1-1/M82	0.93332	1
4-1/M82	0.81283	1
4-3-2/M82	0.81432	0.445
4-3/M82	0.94606	1
5-3/M82	0.99843	1
6-2/M82	0.86087
6-3/M82	0.87877	0.916
7-1/M82	N/A	N/A
7-2/M82	0.9777	1
9-3-2/M82	0.99782

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.40565	0.365
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.21774	0.417
WT/WTpooled	N/A	N/A

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	1.37274	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0475	0.914
DC3000/delta hrp 6h	1.03605	1
DC3000/delta hrp 12h	1.01216	1
DC3000/delta hrp 24h	0.99807	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.10981	0.598
DC3000 delta B/DC3000 delta AB	1.15186	0.311

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.17483	1
Exp 36h	1.38668	0.489
Exp 60h	1.4054	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0058	1
Var 0h	1.26576	0.594
Var 12h I row2-row1	1.38766	0.228
Var 12h NI row2-row1	1.22574	0.34
Var 36h I row2-row1	0.91611	1
Var 36h NI row2-row1	0.72109	0.549
Var 60h I row2-row1	0.86971	0.285
Var 60h NI row2-row1	0.85128	0.572
Time course 0hI-0hNI	1.18992	0.377
Time course 12hI-12hNI	1.85048	0.008
Time course 36hI-36hNI	6.19589	0.004
Time course 60hI-60hNI	9.79448	0.008

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)	1.18196	0.431
transgenic ySAMdc/azygous control (breaker)	0.8409	0.251
transgenic ySAMdc/azygous control (red)	0.92894	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99175	0.459

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.9606	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.24416	0.14
Manapal/WT (break)	1.06699	1
Manapal/WT (red)	0.716	0.242