Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.10.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.77724	0.144
27DAP/17DAP	1.02649	1
39DAP/27DAP	0.88864	0.474
41DAP/39DAP	1.51262	0.293
42DAP/41DAP	0.91232	1
43DAP/42DAP	0.81696	0.705
47DAP/43DAP	0.95349	0.705
52DAP/47DAP	1.90098	0.243
57DAP/52DAP	0.70804	0.513

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12848	0.17
17DAP/reference	0.89286	0.057
27DAP/reference	0.87357	0.019
39DAP/reference	0.8697	0.07
41DAP/reference	0.96718	0.542
42DAP/reference	1.11561	0.174
43DAP/reference	0.99903	0.882
47DAP/reference	0.9863	0.503
52DAP/reference	1.0146	0.668
57DAP/reference	0.91357	0.106

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92345	0.496
27DAP/17DAP	1.04555	0.98
39DAP/27DAP	0.98849	0.932
41DAP/39DAP	1.00259	1
42DAP/41DAP	1.12552	0.622
43DAP/42DAP	1.01872	1
47DAP/43DAP	1.06046	0.884
52DAP/47DAP	0.98134	0.905
57DAP/52DAP	1.01169	0.926
57DAP/7DAP	0.91974	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86949	0.122
17DAP/reference	0.82153	0.014
27DAP/reference	0.75164	0.01
39DAP/reference	0.76314	0.011
41DAP/reference	0.83483	0.03
42DAP/reference	0.82605	0.017
43DAP/reference	0.71551	0.011
47DAP/reference	0.81809	0.101
52DAP/reference	0.81137	0.015
57DAP/reference	0.73411	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.25406	0.049
17DAP/reference	1.40618	0.011
27DAP/reference	1.2754	0.153
39DAP/reference	1.08557	0.806
41DAP/reference	1.03456	1
42DAP/reference	1.08895	0.5
43DAP/reference	1.46005	0.012
47DAP/reference	1.02188	0.775
52DAP/reference	1.20988	0.043
57DAP/reference	1.38871	0.07

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8458	0.082
17DAP/reference	0.99699	0.763
27DAP/reference	0.67443	0.026
39DAP/reference	0.78196	0.043
41DAP/reference	0.90589	0.264
42DAP/reference	1.05228	0.816
43DAP/reference	1.0699	0.88
47DAP/reference	1.01992	1
52DAP/reference	0.77092	0.145
57DAP/reference	1.12674	0.8

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02198	1
26DAP/20DAP	0.8963	0.317
34DAP/26DAP	1.09303	1
51DAP/34DAP	1.13899	0.496
52DAP/51DAP	1.07603	0.556
53DAP/52DAP	1.33232	0.097
55DAP/53DAP	1.06012	0.741
57DAP/55DAP	1.01941	1
62DAP/57DAP	0.99954	1
68DAP/62DAP	0.78477	0.263
68DAP/14DAP	0.83743	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.91568	0.378

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.63471	0.157
Mature Green Tomato/Ripe Tomato	1.04143	0.898
Immature Eggplant/Mature Eggplant	0.72728	0.125
Ripe Pepper/Ripe Tomato	11.1827	1
Mature Eggplant/Ripe Tomato	3.61348	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.11946	0.877
1-1-2/M82	0.91774	1
12-2/M82	1.06771	0.448
12-4/M82	0.94164	1
1-3/M82	1.0554	1
2-1-1/M82	0.95818
2-1/M82	N/A	N/A
2-6/M82	0.95056	1
3-2/M82	0.9899	1
4-1-1/M82	0.98815	1
4-1/M82	0.66139	0.737
4-3-2/M82	0.92898	1
4-3/M82	0.77625
5-3/M82	1.06012	1
6-2/M82	0.94075
6-3/M82	1.08188
7-1/M82	1.17436
7-2/M82	1.09283	1
9-3-2/M82	1.05509	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.93719	1
IL2-6/WTpooled	1.50132
IL7-5/WTpooled	0.89471	1
IL7-3/WTpooled	1.37389	1
IL12-4/WTpooled	1.01855	0.891
IL1-4/WTpooled	1.15969	1
WT/WTpooled	1.12318	0.789

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	0.80584	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00426	1
DC3000/delta hrp 6h	1.22207	1
DC3000/delta hrp 12h	0.96445	1
DC3000/delta hrp 24h	0.83055	0.04

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.60441
DC3000 delta B/DC3000 delta AB	0.69545	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.78133	1
Exp 36h	0.64985	0.623
Exp 60h	0.56822	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01221	1
Var 0h	0.50877	0.274
Var 12h I row2-row1	1.06375	1
Var 12h NI row2-row1	0.97812	0.82
Var 36h I row2-row1	0.92935	0.805
Var 36h NI row2-row1	1.04558	1
Var 60h I row2-row1	1.15442	0.562
Var 60h NI row2-row1	0.99679	1
Time course 0hI-0hNI	0.97581	0.87
Time course 12hI-12hNI	1.01444	1
Time course 36hI-36hNI	0.8507	0.024
Time course 60hI-60hNI	0.43665	0.007

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)	1.19954	0.213
transgenic ySAMdc/azygous control (breaker)	1.35707	0.248
transgenic ySAMdc/azygous control (red)	1.1743	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96114	0.058

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.81511	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.06732	0.088
Manapal/WT (break)	2.26863	0.13
Manapal/WT (red)	2.20857	0.137