Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-5.2.2.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.39708	0.13
27DAP/17DAP	0.97269	0.918
39DAP/27DAP	1.20905	0.601
41DAP/39DAP	0.88631	0.55
42DAP/41DAP	0.91319	1
43DAP/42DAP	1.03096	0.937
47DAP/43DAP	1.30027	0.715
52DAP/47DAP	1.22455	0.819
57DAP/52DAP	1.16062	0.96

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7676	0.048
17DAP/reference	0.89485	0.138
27DAP/reference	0.95762	0.552
39DAP/reference	0.90983	0.17
41DAP/reference	0.78537	0.039
42DAP/reference	0.90992	0.095
43DAP/reference	0.89473	0.211
47DAP/reference	1.03122	0.862
52DAP/reference	1.09798	0.524
57DAP/reference	1.10591	0.321

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.72695	0.036
27DAP/17DAP	1.02757	0.938
39DAP/27DAP	0.92465	0.382
41DAP/39DAP	1.06248	1
42DAP/41DAP	0.97595	0.757
43DAP/42DAP	0.9844	0.831
47DAP/43DAP	0.88835	0.229
52DAP/47DAP	1.03327	0.883
57DAP/52DAP	0.84439	0.28
57DAP/7DAP	1.08888	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2547	0.166
17DAP/reference	1.47216	0.017
27DAP/reference	1.28243	0.06
39DAP/reference	1.38345	0.081
41DAP/reference	1.34405	0.03
42DAP/reference	1.45191	0.014
43DAP/reference	1.55475	0.007
47DAP/reference	1.09856	0.318
52DAP/reference	1.53835	0.026
57DAP/reference	1.25672	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92888	0.426
17DAP/reference	0.96698	0.536
27DAP/reference	1.04842	0.704
39DAP/reference	1.06366	0.806
41DAP/reference	1.13261	0.194
42DAP/reference	1.35496	0.543
43DAP/reference	1.02761	0.761
47DAP/reference	0.91925	0.123
52DAP/reference	1.19961	0.036
57DAP/reference	0.93547	0.361

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14864	0.493
17DAP/reference	1.17011	0.699
27DAP/reference	1.57107	0.021
39DAP/reference	1.42814	0.041
41DAP/reference	1.44836	0.03
42DAP/reference	1.42165	0.054
43DAP/reference	1.478	0.019
47DAP/reference	1.04821	0.901
52DAP/reference	1.78663	0.112
57DAP/reference	1.50012	0.048

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10016	1
26DAP/20DAP	1.43199	0.481
34DAP/26DAP	1.35348	0.542
51DAP/34DAP	0.74059	0.08
52DAP/51DAP	0.67324	0.151
53DAP/52DAP	1.14305	0.23
55DAP/53DAP	0.86961	0.082
57DAP/55DAP	1.18441	0.865
62DAP/57DAP	1.69575	0.007
68DAP/62DAP	0.96368	0.81
68DAP/14DAP	1.06277	0.785

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.12495	0.306

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.62892	0.189
Mature Green Tomato/Ripe Tomato	1.32208	0.106
Immature Eggplant/Mature Eggplant	0.47684	0.047
Ripe Pepper/Ripe Tomato	1.4604	0.258
Mature Eggplant/Ripe Tomato	1.45906	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.21553	0.977
12-2/M82	N/A	N/A
12-4/M82	0.98241	1
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	1.82594	N/A
4-3-2/M82	1.2109	N/A
4-3/M82	N/A	N/A
5-3/M82	0.98085	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.43021	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.00006	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.50143	0.243
IL2-6/WTpooled	0.93411	1
IL7-5/WTpooled	0.94917	1
IL7-3/WTpooled	1.22829	1
IL12-4/WTpooled	1.18248	0.646
IL1-4/WTpooled	0.7729	0.562
WT/WTpooled	1.12997	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	1.09893	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0204	1
DC3000/delta hrp 6h	0.94441	0.95
DC3000/delta hrp 12h	0.93317	1
DC3000/delta hrp 24h	1.09471	0.453

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	3.1357	N/A
DC3000 delta B/DC3000 delta AB	0.83734	0.381

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0637	1
Exp 36h	0.88166	0.623
Exp 60h	0.95796	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97065	1
Var 0h	1.19257	0.98
Var 12h I row2-row1	0.97656	0.948
Var 12h NI row2-row1	0.80038	0.82
Var 36h I row2-row1	1.14443	1
Var 36h NI row2-row1	1.32685	1
Var 60h I row2-row1	1.10286	1
Var 60h NI row2-row1	0.86912	0.292
Time course 0hI-0hNI	1.03208	0.799
Time course 12hI-12hNI	1.00137	1
Time course 36hI-36hNI	0.9034	0.042
Time course 60hI-60hNI	0.9773	0.646

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)	0.88333	0.229
transgenic ySAMdc/azygous control (breaker)	0.80567	0.139
transgenic ySAMdc/azygous control (red)	1.08789	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99053	0.694

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.09047	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.68961	0.172
Manapal/WT (break)	0.7515	0.333
Manapal/WT (red)	1.32248	0.15