Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-1.3.4.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.63712	0.052
27DAP/17DAP	2.05154	0.402
39DAP/27DAP	0.76409	0.399
41DAP/39DAP	1.17221	0.859
42DAP/41DAP	0.90448	1
43DAP/42DAP	0.8896	0.829
47DAP/43DAP	0.76134	0.33
52DAP/47DAP	2.37195	0.126
57DAP/52DAP	0.53815	0.47

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.35158	0.013
17DAP/reference	1.29296	0.013
27DAP/reference	1.1772	0.024
39DAP/reference	0.84578	0.056
41DAP/reference	0.88309	0.154
42DAP/reference	0.89748	0.025
43DAP/reference	1.0956	0.445
47DAP/reference	0.62722	0.001
52DAP/reference	0.65559	0.013
57DAP/reference	0.68897	0.01

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1497	0.87
27DAP/17DAP	0.9149	0.684
39DAP/27DAP	1.01082	1
41DAP/39DAP	1.25437	0.417
42DAP/41DAP	0.92467	0.524
43DAP/42DAP	1.27869	0.112
47DAP/43DAP	1.16171	0.593
52DAP/47DAP	1.14797	0.718
57DAP/52DAP	1.3647	0.11
57DAP/7DAP	1.86278	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98019	0.55
17DAP/reference	0.91214	0.108
27DAP/reference	0.73442	0.01
39DAP/reference	0.77373	0.011
41DAP/reference	0.65218	0.017
42DAP/reference	0.67492	0.011
43DAP/reference	0.78624	0.017
47DAP/reference	0.6962	0.128
52DAP/reference	0.79669	0.053
57DAP/reference	0.68386	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8582	0.204
17DAP/reference	0.96285	0.561
27DAP/reference	1.12674	0.875
39DAP/reference	1.12522	0.182
41DAP/reference	1.02373	1
42DAP/reference	0.92985	0.135
43DAP/reference	0.97193	0.646
47DAP/reference	0.95016	0.319
52DAP/reference	0.72082	0.006
57DAP/reference	0.91168	0.384

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.62383	0.112
17DAP/reference	1.00905	1
27DAP/reference	0.99686	0.805
39DAP/reference	0.81001	0.025
41DAP/reference	0.80577	0.07
42DAP/reference	2.18379	0.053
43DAP/reference	2.06143	0.205
47DAP/reference	0.64757	0.008
52DAP/reference	1.4402	0.534
57DAP/reference	1.08117	0.954

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06207	0.966
26DAP/20DAP	1.10508	0.635
34DAP/26DAP	0.96243	0.927
51DAP/34DAP	1.17749	0.637
52DAP/51DAP	1.23051	0.42
53DAP/52DAP	1.12885	0.806
55DAP/53DAP	1.05371	0.964
57DAP/55DAP	1.00895	0.944
62DAP/57DAP	1.22955	0.767
68DAP/62DAP	0.71012	0.118
68DAP/14DAP	0.64595	0.09

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.41874	0.246

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.26168	0.058
Mature Green Tomato/Ripe Tomato	0.68627	1
Immature Eggplant/Mature Eggplant	0.4413	0.082
Ripe Pepper/Ripe Tomato	0.62576	0.293
Mature Eggplant/Ripe Tomato	0.46996	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.11508	0.591
1-1-2/M82	0.94106	1
12-2/M82	1.68843	0.421
12-4/M82	1.21948	1
1-3/M82	0.9682	1
2-1-1/M82	0.93562	1
2-1/M82	N/A	N/A
2-6/M82	1.15383	0.452
3-2/M82	N/A	N/A
4-1-1/M82	1.02524	1
4-1/M82	1.20605	N/A
4-3-2/M82	1.08289	1
4-3/M82	2.33339	N/A
5-3/M82	0.68898	0.49
6-2/M82	0.91796	1
6-3/M82	0.89516	1
7-1/M82	0.64583	N/A
7-2/M82	1.1381	1
9-3-2/M82	1.17849	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.90599	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.27142	N/A
IL1-4/WTpooled	0.79152	0.834
WT/WTpooled	1.05756	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	1.02934	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96103	N/A
DC3000/delta hrp 6h	1.17793	1
DC3000/delta hrp 12h	1.05341	1
DC3000/delta hrp 24h	0.98052	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	118.346	0.333
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	0.98065	1
Exp 36h	1.00584	1
Exp 60h	0.71841	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.8312	0.289
transgenic ySAMdc/azygous control (breaker)	0.79257	0.251
transgenic ySAMdc/azygous control (red)	1.34216	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.92784	0.054

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.66573	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.98502	1
Manapal/WT (break)	0.98029	1
Manapal/WT (red)	0.94042	0.607