Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.19.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92711	0.617
27DAP/17DAP	1.15183	0.849
39DAP/27DAP	1.10044	0.83
41DAP/39DAP	1.2343	1
42DAP/41DAP	1.35875	0.931
43DAP/42DAP	0.94327	0.77
47DAP/43DAP	0.99198	0.851
52DAP/47DAP	0.92336	0.754
57DAP/52DAP	0.93022	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97524	0.539
17DAP/reference	0.83452	0.026
27DAP/reference	0.91062	0.265
39DAP/reference	0.82188	0.027
41DAP/reference	0.85085	0.085
42DAP/reference	1.02842	0.731
43DAP/reference	0.86159	0.056
47DAP/reference	1.02665	1
52DAP/reference	1.31929	0.014
57DAP/reference	1.12841	0.211

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05839	0.736
27DAP/17DAP	0.95872	0.878
39DAP/27DAP	1.03572	0.758
41DAP/39DAP	0.92709	0.713
42DAP/41DAP	0.99289	0.845
43DAP/42DAP	1.06532	0.554
47DAP/43DAP	1.02339	0.934
52DAP/47DAP	1.13319	0.57
57DAP/52DAP	1.09158	0.917
57DAP/7DAP	0.98658	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95223	0.157
17DAP/reference	0.92615	0.167
27DAP/reference	0.83202	0.048
39DAP/reference	0.8762	0.146
41DAP/reference	0.79444	0.06
42DAP/reference	0.96454	0.458
43DAP/reference	0.91932	0.252
47DAP/reference	0.8877	0.383
52DAP/reference	0.74277	0.024
57DAP/reference	1.00475	0.629

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86626	0.214
17DAP/reference	0.88256	0.109
27DAP/reference	1.03435	1
39DAP/reference	1.20553	0.556
41DAP/reference	1.7055	0.014
42DAP/reference	1.15587	0.17
43DAP/reference	0.74873	0.092
47DAP/reference	0.85823	0.027
52DAP/reference	1.17154	0.01
57DAP/reference	0.78309	0.024

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83932	0.087
17DAP/reference	0.83482	0.099
27DAP/reference	1.07357	0.248
39DAP/reference	0.92889	0.133
41DAP/reference	0.95168	0.512
42DAP/reference	1.27928	0.258
43DAP/reference	1.1394	0.7
47DAP/reference	1.04783	0.754
52DAP/reference	1.11323	0.854
57DAP/reference	1.69265	0.09

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06937	0.966
26DAP/20DAP	0.90438	0.223
34DAP/26DAP	0.98348	0.98
51DAP/34DAP	0.88857	0.631
52DAP/51DAP	1.17155	0.783
53DAP/52DAP	0.86394	0.133
55DAP/53DAP	1.09551	0.722
57DAP/55DAP	0.88715	0.479
62DAP/57DAP	1.26435	0.303
68DAP/62DAP	2.07649	0.054
68DAP/14DAP	2.19012	0.027

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.08518	0.558

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.26036	0.287
Mature Green Tomato/Ripe Tomato	1.88436	0.044
Immature Eggplant/Mature Eggplant	0.70449	0.105
Ripe Pepper/Ripe Tomato	1.34712
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	0.92756
12-2/M82	1.15115
12-4/M82	0.90624	0.274
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	1.44482
3-2/M82	N/A	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	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.12206
7-2/M82	0.72858
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.11017
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.22195	0.792
IL7-3/WTpooled	2.04063
IL12-4/WTpooled	0.88007	0.71
IL1-4/WTpooled	1.00406	1
WT/WTpooled	1.12812	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	0.7989	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97657	1
DC3000/delta hrp 6h	0.93604	0.95
DC3000/delta hrp 12h	1.12996	1
DC3000/delta hrp 24h	1.19241	0.467

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.59963
DC3000 delta B/DC3000 delta AB	1.46715	0.215

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04189	1
Exp 36h	0.8683	0.449
Exp 60h	0.97777	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98546	1
Var 0h	1.02768	1
Var 12h I row2-row1	0.89035	0.467
Var 12h NI row2-row1	1.08198	1
Var 36h I row2-row1	0.91082	1
Var 36h NI row2-row1	1.04678	1
Var 60h I row2-row1	1.24897	1
Var 60h NI row2-row1	1.10955	0.904
Time course 0hI-0hNI	1.00952	0.867
Time course 12hI-12hNI	3.1219	0.512
Time course 36hI-36hNI	1.19638	0.039
Time course 60hI-60hNI	1.20043	0.029

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)	1.09826	0.612
transgenic ySAMdc/azygous control (breaker)	0.97621	1
transgenic ySAMdc/azygous control (red)	0.92419	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.91998	0.05

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.31981	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.35776	0.09
Manapal/WT (break)	1.11107	0.381
Manapal/WT (red)	1.56882	0.164