Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.6.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83868	0.089
27DAP/17DAP	0.80724	0.575
39DAP/27DAP	0.96564	0.67
41DAP/39DAP	1.29636	0.331
42DAP/41DAP	1.25642	0.873
43DAP/42DAP	0.9502	0.892
47DAP/43DAP	0.96509	0.851
52DAP/47DAP	1.15201	0.821
57DAP/52DAP	0.66587	0.462

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09959	0.265
17DAP/reference	1.04279	0.342
27DAP/reference	0.97699	0.595
39DAP/reference	0.90845	0.068
41DAP/reference	0.91091	0.065
42DAP/reference	0.96739	0.259
43DAP/reference	1.01082	0.812
47DAP/reference	0.93522	0.161
52DAP/reference	0.89668	0.043
57DAP/reference	0.90921	0.018

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99151	0.801
27DAP/17DAP	1.10731	0.768
39DAP/27DAP	0.89768	0.103
41DAP/39DAP	1.28117	0.036
42DAP/41DAP	0.91123	0.404
43DAP/42DAP	0.87138	0.04
47DAP/43DAP	1.03419	0.906
52DAP/47DAP	0.88981	0.439
57DAP/52DAP	0.86564	0.115
57DAP/7DAP	0.78266

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28464	0.124
17DAP/reference	1.24371	0.162
27DAP/reference	1.21201	0.008
39DAP/reference	1.40285	0.014
41DAP/reference	1.38124	0.057
42DAP/reference	1.23059	0.076
43DAP/reference	1.03938	0.672
47DAP/reference	1.06396	0.571
52DAP/reference	1.3206	0.017
57DAP/reference	1.23763	0.04

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02885	0.894
17DAP/reference	1.0444	0.531
27DAP/reference	0.98648	0.642
39DAP/reference	1.07129	0.602
41DAP/reference	0.91991	0.057
42DAP/reference	0.93811	0.121
43DAP/reference	1.02959	0.89
47DAP/reference	0.93109	0.035
52DAP/reference	0.92277	0.111
57DAP/reference	1.11714	0.523

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31847	0.064
17DAP/reference	1.01099	0.988
27DAP/reference	0.96676	0.566
39DAP/reference	1.28227	0.151
41DAP/reference	1.46091	0.062
42DAP/reference	1.1642	0.45
43DAP/reference	1.34416	0.19
47DAP/reference	1.06452	0.73
52DAP/reference	1.10929	0.405
57DAP/reference	1.10007	0.531

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99296	1
26DAP/20DAP	1.55446	0.223
34DAP/26DAP	1.13551	0.819
51DAP/34DAP	0.6094	0.106
52DAP/51DAP	1.04363	0.873
53DAP/52DAP	0.79293	0.475
55DAP/53DAP	1.04526	0.951
57DAP/55DAP	1.15822	0.424
62DAP/57DAP	1.01289	1
68DAP/62DAP	1.07879	0.878
68DAP/14DAP	0.96219	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.91196	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	2.56114	0.016
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.52946	0.224
Mature Eggplant/Ripe Tomato	1.1755	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.88968	0.536
1-1-2/M82	0.92136
12-2/M82	1.28165	1
12-4/M82	0.90023	1
1-3/M82	0.94845	1
2-1-1/M82	1.20848	0.764
2-1/M82	N/A	N/A
2-6/M82	1.07155	0.695
3-2/M82	N/A	N/A
4-1-1/M82	1.15245
4-1/M82	1.6517
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.90394	0.49
6-2/M82	0.91145	1
6-3/M82	1.206
7-1/M82	N/A	N/A
7-2/M82	0.958	1
9-3-2/M82	0.91501

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.71755
IL2-6/WTpooled	0.94228
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.76367
IL12-4/WTpooled	0.99785	1
IL1-4/WTpooled	1.16218
WT/WTpooled	1.09621	0.999

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	1.08723	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92711	0.807
DC3000/delta hrp 6h	0.50767
DC3000/delta hrp 12h	1.34757	1
DC3000/delta hrp 24h	0.94453	0.523

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.06684	0.648
DC3000 delta B/DC3000 delta AB	1.1666	0.462

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04534	1
Exp 36h	1.52533	1
Exp 60h	1.29823	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02096
Var 0h	0.51115	1
Var 12h I row2-row1	0.95448	0.856
Var 12h NI row2-row1	1.21234	0.649
Var 36h I row2-row1	0.99769	1
Var 36h NI row2-row1	1.0009	1
Var 60h I row2-row1	1.03754	1
Var 60h NI row2-row1	0.86604	0.408
Time course 0hI-0hNI	0.91052	0.294
Time course 12hI-12hNI	1.01798	0.777
Time course 36hI-36hNI	1.10797	0.355
Time course 60hI-60hNI	1.0618	0.426

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)	1.05557	1
transgenic ySAMdc/azygous control (breaker)	0.55235	0.129
transgenic ySAMdc/azygous control (red)	0.97737	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93824	0.058

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.73077	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.76086	1
Manapal/WT (break)	1.01903	1
Manapal/WT (red)	0.80039	0.242