Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.20.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.42078	0.63
27DAP/17DAP	0.95501	0.99
39DAP/27DAP	0.81201	0.462
41DAP/39DAP	1.55463	0.37
42DAP/41DAP	1.17418	0.871
43DAP/42DAP	1.09728	1
47DAP/43DAP	1.23148	0.689
52DAP/47DAP	1.78117	0.421
57DAP/52DAP	1.53286	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09142	0.218
17DAP/reference	0.9907	0.737
27DAP/reference	0.99858	0.885
39DAP/reference	1.01535	0.352
41DAP/reference	1.01017	0.624
42DAP/reference	1.13675	0.007
43DAP/reference	1.0054	0.957
47DAP/reference	1.03962	0.379
52DAP/reference	1.13145	0.286
57DAP/reference	1.05796	0.355

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02504	0.785
27DAP/17DAP	0.97767	0.782
39DAP/27DAP	0.95968	0.536
41DAP/39DAP	1.01883	0.837
42DAP/41DAP	0.99721	0.924
43DAP/42DAP	0.98682	0.831
47DAP/43DAP	1.00219	0.973
52DAP/47DAP	1.01041	0.973
57DAP/52DAP	0.94658	0.426
57DAP/7DAP	0.91627	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93229	0.157
17DAP/reference	0.89046	0.012
27DAP/reference	0.93526	0.042
39DAP/reference	0.9224	0.023
41DAP/reference	0.92296	0.086
42DAP/reference	1.00157	1
43DAP/reference	0.92793	0.049
47DAP/reference	0.90935	0.128
52DAP/reference	1.06408	0.052
57DAP/reference	1.04021	0.5

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01961	0.477
17DAP/reference	1.09453	0.033
27DAP/reference	1.11475	0.516
39DAP/reference	1.0365	0.806
41DAP/reference	0.94937	0.242
42DAP/reference	1.04651	0.596
43DAP/reference	1.17367	0.025
47DAP/reference	1.0004	0.833
52DAP/reference	1.02313	0.559
57DAP/reference	0.96052	0.226

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87549	0.063
17DAP/reference	0.97978	0.647
27DAP/reference	0.85781	0.049
39DAP/reference	0.84009	0.012
41DAP/reference	0.93346	0.132
42DAP/reference	0.93086	0.049
43DAP/reference	0.90935	0.12
47DAP/reference	0.97916	0.465
52DAP/reference	0.89205	0.296
57DAP/reference	0.95759	0.468

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98378	1
26DAP/20DAP	0.92727	0.244
34DAP/26DAP	0.9981	1
51DAP/34DAP	0.94095	0.618
52DAP/51DAP	1.02711	0.842
53DAP/52DAP	0.98425	0.938
55DAP/53DAP	1.1036	0.737
57DAP/55DAP	0.97645	0.909
62DAP/57DAP	1.00772	1
68DAP/62DAP	0.95059	0.769
68DAP/14DAP	1.22894	0.453

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02935	0.7

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.89266	0.401
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.80295	0.05
Ripe Pepper/Ripe Tomato	1.54337	1
Mature Eggplant/Ripe Tomato	2.26283	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.08492	0.877
1-1-2/M82	1.03314	1
12-2/M82	0.97546	0.955
12-4/M82	0.97624
1-3/M82	0.97442	0.501
2-1-1/M82	1.0083	1
2-1/M82	1.0387
2-6/M82	0.9448	1
3-2/M82	1.07078
4-1-1/M82	1.09392	0.876
4-1/M82	0.96261
4-3-2/M82	1.2075
4-3/M82	1.02332	1
5-3/M82	1.03857	1
6-2/M82	1.00454	1
6-3/M82	1.00632	1
7-1/M82	1.06472
7-2/M82	0.85631	0.796
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	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	N/A	N/A
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	1.22017	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04838	0.921
DC3000/delta hrp 6h	1.10685	1
DC3000/delta hrp 12h	0.97742	1
DC3000/delta hrp 24h	0.97685	0.875

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.00818	0.556
DC3000 delta B/DC3000 delta AB	1.06206	0.437

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.37551	1
Exp 36h	0.93489	0.82
Exp 60h	0.97491	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03612	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.11477	0.654
Var 12h NI row2-row1	1.08089	1
Var 36h I row2-row1	0.98989	1
Var 36h NI row2-row1	0.87289	0.645
Var 60h I row2-row1	1.00316	1
Var 60h NI row2-row1	1.09606	0.904
Time course 0hI-0hNI	1.04993	0.451
Time course 12hI-12hNI	1.00452	0.888
Time course 36hI-36hNI	0.98176	0.54
Time course 60hI-60hNI	1.20092	0.029

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)	0.8111	0.306
transgenic ySAMdc/azygous control (breaker)	0.75143	0.173
transgenic ySAMdc/azygous control (red)	1.00228	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05083	0.261

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.77716	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.17844	0.307
Manapal/WT (break)	0.92405	0.333
Manapal/WT (red)	0.97757	0.863