Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.7.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.72214	0.166
27DAP/17DAP	0.97335	0.973
39DAP/27DAP	1.32028	0.252
41DAP/39DAP	0.93413	0.726
42DAP/41DAP	0.97376	1
43DAP/42DAP	1.05635	1
47DAP/43DAP	1.12806	0.776
52DAP/47DAP	1.27533	0.646
57DAP/52DAP	1.20826	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89946	0.39
17DAP/reference	0.68798	0.129
27DAP/reference	1.0886	0.696
39DAP/reference	1.03044	0.92
41DAP/reference	0.8182	0.085
42DAP/reference	1.09667	0.812
43DAP/reference	1.02637	0.957
47DAP/reference	1.16112	0.243
52DAP/reference	1.45521	0.015
57DAP/reference	1.63998	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.76992	0.35
27DAP/17DAP	1.2193	0.506
39DAP/27DAP	0.95807	0.712
41DAP/39DAP	1.03344	0.861
42DAP/41DAP	1.02624	0.984
43DAP/42DAP	1.08311	0.746
47DAP/43DAP	1.1355	0.765
52DAP/47DAP	0.91164	0.694
57DAP/52DAP	0.97461	0.75
57DAP/7DAP	1.68162	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.31992	0.032
17DAP/reference	2.45988	0.006
27DAP/reference	2.85745	0.006
39DAP/reference	4.33069	0.005
41DAP/reference	3.85509	0.011
42DAP/reference	5.74886	0.006
43DAP/reference	4.50666	0.006
47DAP/reference	2.48445	0.02
52DAP/reference	3.48392	0.007
57DAP/reference	3.1748	0.003

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97717	0.736
17DAP/reference	0.96033	0.487
27DAP/reference	1.21417	0.225
39DAP/reference	1.27799	0.106
41DAP/reference	1.61864	0.006
42DAP/reference	1.25025	0.102
43DAP/reference	0.78013	0.075
47DAP/reference	1.09889	0.621
52DAP/reference	0.99806	0.713
57DAP/reference	0.85585	0.068

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.67557	0.03
17DAP/reference	1.20143	0.689
27DAP/reference	2.36211	0.024
39DAP/reference	2.41458	0.012
41DAP/reference	1.83605	0.012
42DAP/reference	3.03915	0.007
43DAP/reference	2.6294	0.007
47DAP/reference	1.17336	0.355
52DAP/reference	4.69936	0.032
57DAP/reference	4.14164	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.19811	1
26DAP/20DAP	0.9899	1
34DAP/26DAP	1.23363	1
51DAP/34DAP	0.95665	0.598
52DAP/51DAP	1.30562	0.186
53DAP/52DAP	0.67205	0.254
55DAP/53DAP	1.19214	0.671
57DAP/55DAP	0.81206	0.458
62DAP/57DAP	0.73602
68DAP/62DAP	0.87829	0.787
68DAP/14DAP	1.61179	0.025

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.34234	0.591

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.74306	0.119
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.46451	0.224
Mature Eggplant/Ripe Tomato	0.31831	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.82015	0.934
1-1-2/M82	1.15378	1
12-2/M82	0.75226	0.639
12-4/M82	0.82458	0.358
1-3/M82	N/A	N/A
2-1-1/M82	1.01063	1
2-1/M82	N/A	N/A
2-6/M82	1.40862	0.329
3-2/M82	N/A	N/A
4-1-1/M82	1.19078	1
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.01319	1
5-3/M82	1.20431	1
6-2/M82	1.08682
6-3/M82	1.02511
7-1/M82	N/A	N/A
7-2/M82	1.17557	1
9-3-2/M82	1.1779

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.26054	0.277
IL2-6/WTpooled	0.77269	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.6148	0.362
IL12-4/WTpooled	1.19788	0.737
IL1-4/WTpooled	1.098	1
WT/WTpooled	0.98672	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	1.03557	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.1006	0.758
DC3000/delta hrp 6h	0.94566	0.95
DC3000/delta hrp 12h	0.92331	1
DC3000/delta hrp 24h	0.90183	0.438

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.96827
DC3000 delta B/DC3000 delta AB	1.0099	1

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	1.18724	1
Var 0h	0.75804	0.261
Var 12h I row2-row1	0.91917	0.39
Var 12h NI row2-row1	1.19012	0.34
Var 36h I row2-row1	1.37741	0.742
Var 36h NI row2-row1	0.63848	0.478
Var 60h I row2-row1	1.11491	1
Var 60h NI row2-row1	0.86668	0.818
Time course 0hI-0hNI	0.99312	1
Time course 12hI-12hNI	1.00884	0.888
Time course 36hI-36hNI	1.21924	0.101
Time course 60hI-60hNI	0.958	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)	0.92823	0.377
transgenic ySAMdc/azygous control (breaker)	1.53023	0.161
transgenic ySAMdc/azygous control (red)	1.0915	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.1964	0.213

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.46746	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.07579	1
Manapal/WT (break)	0.83599	1
Manapal/WT (red)	0.93247	0.503