Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-5.2.16.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.93046	0.205
27DAP/17DAP	1.71046	0.618
39DAP/27DAP	1.46926	0.214
41DAP/39DAP	0.89301	0.552
42DAP/41DAP	1.05823	1
43DAP/42DAP	1.19009	1
47DAP/43DAP	1.74497	0.285
52DAP/47DAP	0.77017	0.461
57DAP/52DAP	1.70622	0.77

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92874	0.336
17DAP/reference	0.78107	0.009
27DAP/reference	1.05711	0.863
39DAP/reference	0.77755	0.047
41DAP/reference	0.60585	0.009
42DAP/reference	1.01442	0.547
43DAP/reference	0.893	0.042
47DAP/reference	1.0531	0.646
52DAP/reference	1.44568	0.045
57DAP/reference	1.39307	0.01

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.35205	0.051
27DAP/17DAP	1.01096	0.969
39DAP/27DAP	1.14672	0.241
41DAP/39DAP	0.93362	0.465
42DAP/41DAP	1.02533	0.991
43DAP/42DAP	0.95179	0.538
47DAP/43DAP	1.16379	0.414
52DAP/47DAP	1.00882	1
57DAP/52DAP	1.07493	0.718
57DAP/7DAP	1.58913	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.81928	0.03
17DAP/reference	2.51801	0.006
27DAP/reference	1.95998	0.007
39DAP/reference	2.76877	0.005
41DAP/reference	2.232	0.034
42DAP/reference	2.60237	0.006
43DAP/reference	4.13375	0.006
47DAP/reference	2.12016	0.054
52DAP/reference	2.17696	0.007
57DAP/reference	2.81934	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75196	0.029
17DAP/reference	0.80429	0.01
27DAP/reference	1.0224	0.663
39DAP/reference	1.21417	0.355
41DAP/reference	1.33283	0.088
42DAP/reference	1.12684	0.288
43DAP/reference	0.56687	0.014
47DAP/reference	0.76396	0.025
52DAP/reference	1.01659	1
57DAP/reference	0.63237	0.008

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.75559	0.026
17DAP/reference	1.26003	0.675
27DAP/reference	2.45791	0.02
39DAP/reference	2.11578	0.017
41DAP/reference	2.05702	0.007
42DAP/reference	2.20653	0.006
43DAP/reference	2.43946	0.007
47DAP/reference	1.31045	0.405
52DAP/reference	2.34025	0.094
57DAP/reference	2.68385	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.24518	0.966
26DAP/20DAP	1.08057	0.818
34DAP/26DAP	1.42217	0.819
51DAP/34DAP	1.21444	0.55
52DAP/51DAP	0.79092	0.151
53DAP/52DAP	2.3091	0.021
55DAP/53DAP	1.27236	0.29
57DAP/55DAP	0.97132	0.854
62DAP/57DAP	0.77411	0.466
68DAP/62DAP	2.68915	0.034
68DAP/14DAP	4.1959	0.03

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.26655	0.198

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.81705	0.274
Mature Green Tomato/Ripe Tomato	0.97706	0.715
Immature Eggplant/Mature Eggplant	0.69669	0.065
Ripe Pepper/Ripe Tomato	1.72169	0.235
Mature Eggplant/Ripe Tomato	2.0338	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.74397	N/A
12-2/M82	N/A	N/A
12-4/M82	0.96891	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	0.97991	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.20129	N/A
4-3-2/M82	0.94976	1
4-3/M82	0.89213	1
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.04219	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.972	1
IL2-6/WTpooled	1.18559	0.395
IL7-5/WTpooled	0.54105	1
IL7-3/WTpooled	0.88626	0.31
IL12-4/WTpooled	1.04451	0.891
IL1-4/WTpooled	1.07443	0.426
WT/WTpooled	1.05344	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	0.97786	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.86721	1
DC3000/delta hrp 6h	1.0947	1
DC3000/delta hrp 12h	1.27451	1
DC3000/delta hrp 24h	0.87503	0.379

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.78986	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04746	1
Exp 36h	0.98309	1
Exp 60h	0.94702	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01447	1
Var 0h	1.81994	0.782
Var 12h I row2-row1	0.96951	0.77
Var 12h NI row2-row1	1.00095	1
Var 36h I row2-row1	1.20823	0.601
Var 36h NI row2-row1	0.73043	0.61
Var 60h I row2-row1	0.97977	0.952
Var 60h NI row2-row1	0.93328	0.292
Time course 0hI-0hNI	1.0817	0.63
Time course 12hI-12hNI	1.02518	0.777
Time course 36hI-36hNI	0.94298	0.171
Time course 60hI-60hNI	0.89096	0.047

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)	0.96546	0.314
transgenic ySAMdc/azygous control (breaker)	1.12873	0.248
transgenic ySAMdc/azygous control (red)	0.97588	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.13202	0.301

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.46491	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.7216	0.096
Manapal/WT (break)	1.99382	0.14
Manapal/WT (red)	1.55748	0.222