Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.12.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84097	0.111
27DAP/17DAP	0.96135	0.964
39DAP/27DAP	1.0292	1
41DAP/39DAP	1.04731	0.535
42DAP/41DAP	1.1194	0.813
43DAP/42DAP	0.99565	0.937
47DAP/43DAP	0.81149	0.433
52DAP/47DAP	1.30568	0.453
57DAP/52DAP	1.00585	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2833	0.021
17DAP/reference	1.06219	0.22
27DAP/reference	1.00176	1
39DAP/reference	1.04927	0.524
41DAP/reference	1.13196	0.085
42DAP/reference	1.23043	0.001
43DAP/reference	1.05924	0.382
47DAP/reference	1.20229	0.003
52DAP/reference	1.14386	0.167
57DAP/reference	1.04743	0.463

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	N/A	N/A
27DAP/17DAP	N/A	N/A
39DAP/27DAP	0.97338
41DAP/39DAP	1.00197	1
42DAP/41DAP	1.04749	0.879
43DAP/42DAP	N/A	N/A
47DAP/43DAP	0.97153	0.774
52DAP/47DAP	0.96525	0.898
57DAP/52DAP	1.04651	0.858
57DAP/7DAP	1.05605	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08463	0.705
17DAP/reference	0.94605	0.044
27DAP/reference	0.99198	0.571
39DAP/reference	0.96281	0.109
41DAP/reference	0.95262	0.271
42DAP/reference	0.96472	0.32
43DAP/reference	0.95015	0.192
47DAP/reference	1.07491	0.468
52DAP/reference	0.94103	0.163
57DAP/reference	0.91134	0.074

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.33089	0.102
17DAP/reference	1.54736	0.019
27DAP/reference	1.45345	0.031
39DAP/reference	1.44052	0.038
41DAP/reference	1.57077	0.015
42DAP/reference	1.21234	0.19
43DAP/reference	1.44658	0.089
47DAP/reference	1.19615	0.153
52DAP/reference	1.15934	0.008
57DAP/reference	1.25334	0.048

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0374	0.356
17DAP/reference	1.13474	0.585
27DAP/reference	0.94652	0.337
39DAP/reference	1.00895	0.813
41DAP/reference	1.01597	1
42DAP/reference	1.28907	0.226
43DAP/reference	1.37043	0.098
47DAP/reference	1.28876	0.187
52DAP/reference	1.10127	0.463
57DAP/reference	1.32806	0.104

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93939	1
26DAP/20DAP	1.17733	0.366
34DAP/26DAP	0.88108	0.387
51DAP/34DAP	0.9187	0.286
52DAP/51DAP	1.00956	0.873
53DAP/52DAP	1.10066	0.768
55DAP/53DAP	0.86487
57DAP/55DAP	1.07622	0.87
62DAP/57DAP	1.01409	1
68DAP/62DAP	0.88506	0.7
68DAP/14DAP	1.13418	0.179

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.18941	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.88137	0.384
Mature Green Tomato/Ripe Tomato	1.16291
Immature Eggplant/Mature Eggplant	1.38916	0.074
Ripe Pepper/Ripe Tomato	0.91755	1
Mature Eggplant/Ripe Tomato	0.8064	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05453	0.591
1-1-2/M82	0.98465	1
12-2/M82	0.97036	0.955
12-4/M82	1.02923	1
1-3/M82	1.1496
2-1-1/M82	0.87667
2-1/M82	1.18489
2-6/M82	1.06053	0.329
3-2/M82	1.02824	1
4-1-1/M82	1.01166	1
4-1/M82	1.15737	0.853
4-3-2/M82	1.19691	0.246
4-3/M82	1.05393	1
5-3/M82	1.1197	1
6-2/M82	0.96064	1
6-3/M82	1.01297	1
7-1/M82	0.93833	1
7-2/M82	1.10973	0.385
9-3-2/M82	1.19726	1

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	1.14675	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02335	0.921
DC3000/delta hrp 6h	1.0357	0.95
DC3000/delta hrp 12h	0.97125	1
DC3000/delta hrp 24h	1.1263	0.483

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.07469	0.068
DC3000 delta B/DC3000 delta AB	1.0681	0.453

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.85839	1
Exp 36h	1.10221	1
Exp 60h	1.29681	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02036	1
Var 0h	0.74937	1
Var 12h I row2-row1	1.10233	0.296
Var 12h NI row2-row1	1.10711	0.34
Var 36h I row2-row1	0.86655	1
Var 36h NI row2-row1	0.84489	0.329
Var 60h I row2-row1	0.98289	0.832
Var 60h NI row2-row1	1.04281	1
Time course 0hI-0hNI	1.07217	0.764
Time course 12hI-12hNI	1.05443	0.467
Time course 36hI-36hNI	1.2031	0.044
Time course 60hI-60hNI	1.67096	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)	0.96429	0.362
transgenic ySAMdc/azygous control (breaker)	1.58037	0.248
transgenic ySAMdc/azygous control (red)	1.29428	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02951	0.213

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.69226	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89822	1
Manapal/WT (break)	1.11533	0.381
Manapal/WT (red)	1.38635	0.222