Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-6.2.9.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.79303	0.221
27DAP/17DAP	0.82735	0.606
39DAP/27DAP	1.10286	0.83
41DAP/39DAP	0.76374	0.362
42DAP/41DAP	2.07538	0.262
43DAP/42DAP	1.36353	0.772
47DAP/43DAP	0.85719	0.51
52DAP/47DAP	0.93793	0.789
57DAP/52DAP	1.42344	0.737

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83696	0.154
17DAP/reference	0.96265	0.567
27DAP/reference	0.84496	0.141
39DAP/reference	1.06216	0.857
41DAP/reference	0.87251	0.341
42DAP/reference	1.05676	0.384
43DAP/reference	0.99523	0.861
47DAP/reference	0.80653	0.015
52DAP/reference	0.85471	0.042
57DAP/reference	0.95381	0.308

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.21406	0.91
27DAP/17DAP	0.98437	0.943
39DAP/27DAP	0.86674	0.4
41DAP/39DAP	0.82155	0.567
42DAP/41DAP	1.07626	1
43DAP/42DAP	1.04266	0.699
47DAP/43DAP	0.88646	0.588
52DAP/47DAP	1.32081	0.444
57DAP/52DAP	0.71735	N/A
57DAP/7DAP	1.49504	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77937	0.062
17DAP/reference	0.82281	0.024
27DAP/reference	0.76981	0.011
39DAP/reference	0.78698	0.011
41DAP/reference	0.7382	0.023
42DAP/reference	0.64313	0.01
43DAP/reference	0.58115	0.012
47DAP/reference	0.70506	0.128
52DAP/reference	0.59418	0.012
57DAP/reference	0.74188	0.064

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09916	0.863
17DAP/reference	1.25967	0.924
27DAP/reference	0.90231	0.123
39DAP/reference	0.93215	0.322
41DAP/reference	0.81913	0.042
42DAP/reference	0.89413	0.135
43DAP/reference	0.97838	0.633
47DAP/reference	0.8337	0.03
52DAP/reference	1.00895	1
57DAP/reference	0.97679	0.61

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83417	0.047
17DAP/reference	0.92078	0.262
27DAP/reference	0.7984	0.025
39DAP/reference	0.81024	0.023
41DAP/reference	0.85262	0.037
42DAP/reference	0.79153	0.018
43DAP/reference	0.84046	0.125
47DAP/reference	0.87322	0.168
52DAP/reference	0.90016	0.424
57DAP/reference	0.97143	0.553

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.28196	0.916
26DAP/20DAP	1.29242	0.477
34DAP/26DAP	0.99854	1
51DAP/34DAP	0.86724	0.394
52DAP/51DAP	0.96392	1
53DAP/52DAP	1.13788	0.783
55DAP/53DAP	1.04534	0.964
57DAP/55DAP	0.98721	0.923
62DAP/57DAP	1.07	0.393
68DAP/62DAP	0.82578	0.543
68DAP/14DAP	1.36317	0.051

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.87572	0.224

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.94501	0.648
Mature Green Tomato/Ripe Tomato	1.16769	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	13.3748	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.90278	N/A
12-2/M82	N/A	N/A
12-4/M82	0.95992	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	0.84189	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.96726	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	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	1.24875	0.659
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.65721	0.362
IL12-4/WTpooled	1.92291	0.522
IL1-4/WTpooled	1.00305	N/A
WT/WTpooled	0.94579	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	0.80083	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.13056	0.921
DC3000/delta hrp 6h	0.48359	N/A
DC3000/delta hrp 12h	0.99502	1
DC3000/delta hrp 24h	0.93521	0.654

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.11709	1
Var 0h	1.1197	0.782
Var 12h I row2-row1	1.16556	0.654
Var 12h NI row2-row1	1.01571	1
Var 36h I row2-row1	0.43492	1
Var 36h NI row2-row1	0.76228	0.645
Var 60h I row2-row1	1.06254	1
Var 60h NI row2-row1	0.95526	1
Time course 0hI-0hNI	0.77803	0.233
Time course 12hI-12hNI	1.98949	0.467
Time course 36hI-36hNI	0.88697	0.206
Time course 60hI-60hNI	0.67053	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)	1.0864	0.748
transgenic ySAMdc/azygous control (breaker)	1.26074	0.248
transgenic ySAMdc/azygous control (red)	1.381	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.92191	0.058

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.66398	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.11902	1
Manapal/WT (break)	1.11552	1
Manapal/WT (red)	1.3945	0.222