Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.14.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03205	0.878
27DAP/17DAP	1.01062	0.92
39DAP/27DAP	1.0649	0.946
41DAP/39DAP	1.04525	0.553
42DAP/41DAP	0.96007	1
43DAP/42DAP	1.02467	1
47DAP/43DAP	1.01671	0.856
52DAP/47DAP	1.16589	0.724
57DAP/52DAP	1.0495	0.787

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95369	0.422
17DAP/reference	0.99455	0.858
27DAP/reference	0.96401	0.497
39DAP/reference	0.89074	0.064
41DAP/reference	0.94375	0.114
42DAP/reference	0.88957	0.009
43DAP/reference	0.98992	0.805
47DAP/reference	1.00304	0.764
52DAP/reference	0.97385	0.449
57DAP/reference	1.0565	0.682

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04369	0.464
27DAP/17DAP	0.96599	0.748
39DAP/27DAP	0.98714	0.925
41DAP/39DAP	1.02506	0.817
42DAP/41DAP	1.00132	0.939
43DAP/42DAP	1.08301	0.03
47DAP/43DAP	1.00976	0.951
52DAP/47DAP	1.05719	0.789
57DAP/52DAP	0.97106	0.651
57DAP/7DAP	0.98353	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02821	0.747
17DAP/reference	0.96671	0.167
27DAP/reference	0.99516	0.656
39DAP/reference	0.98102	0.056
41DAP/reference	0.93328	0.107
42DAP/reference	0.97294	0.117
43DAP/reference	0.94355	0.1
47DAP/reference	1.051	0.745
52DAP/reference	0.97545	0.332
57DAP/reference	0.94062	0.056

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89352	0.034
17DAP/reference	0.84289	0.006
27DAP/reference	0.90771	0.09
39DAP/reference	0.87587	0.081
41DAP/reference	0.79679	0.008
42DAP/reference	0.90217	0.028
43DAP/reference	0.86128	0.046
47DAP/reference	0.93695	0.099
52DAP/reference	0.79385	0.007
57DAP/reference	0.81479	0.035

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02508	0.631
17DAP/reference	1.02702	0.746
27DAP/reference	1.04191	0.51
39DAP/reference	0.97346	0.464
41DAP/reference	0.98168	0.167
42DAP/reference	1.01505	0.759
43DAP/reference	0.95531	0.305
47DAP/reference	0.84368	0.016
52DAP/reference	0.91405	0.169
57DAP/reference	1.10904	0.223

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04788	0.966
26DAP/20DAP	1.02829	0.941
34DAP/26DAP	1.06507	0.19
51DAP/34DAP	1.01497	0.869
52DAP/51DAP	0.97627	1
53DAP/52DAP	1.0361	0.882
55DAP/53DAP	1.00021	0.908
57DAP/55DAP	1.10277	0.826
62DAP/57DAP	0.87074	0.162
68DAP/62DAP	1.07927	0.956
68DAP/14DAP	1.12059	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.95863	0.493

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.64684	0.168
Mature Green Tomato/Ripe Tomato	0.91129	0.446
Immature Eggplant/Mature Eggplant	1.87343	0.05
Ripe Pepper/Ripe Tomato	1.45628	1
Mature Eggplant/Ripe Tomato	0.74164

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9628	0.944
1-1-2/M82	0.96906	1
12-2/M82	0.94773	0.955
12-4/M82	0.96051	0.619
1-3/M82	0.99112	1
2-1-1/M82	0.81305	0.465
2-1/M82	0.96724	1
2-6/M82	0.96512	1
3-2/M82	0.93661	1
4-1-1/M82	1.07622	1
4-1/M82	0.88184	1
4-3-2/M82	0.90258	1
4-3/M82	0.97539	1
5-3/M82	0.94171	1
6-2/M82	1.00732	1
6-3/M82	1.00805	1
7-1/M82	0.99439	1
7-2/M82	0.96641	0.881
9-3-2/M82	0.94144	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.12599	0.395
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.85964	0.418
IL12-4/WTpooled	1.19697	0.624
IL1-4/WTpooled	1.16804	0.395
WT/WTpooled	1.06691	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	1.02714	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02957	0.921
DC3000/delta hrp 6h	1.02215	1
DC3000/delta hrp 12h	1.007	1
DC3000/delta hrp 24h	1.00794	0.84

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.07145	0.145
DC3000 delta B/DC3000 delta AB	1.12287	0.341

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.13077	0.254
Exp 36h	1.12328	1
Exp 60h	1.58268	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98244	1
Var 0h	0.57141	0.339
Var 12h I row2-row1	1.08773	0.473
Var 12h NI row2-row1	0.95184	0.82
Var 36h I row2-row1	1.05417	1
Var 36h NI row2-row1	1.00835	1
Var 60h I row2-row1	1.31261	0.562
Var 60h NI row2-row1	1.20407	0.904
Time course 0hI-0hNI	0.92354	0.386
Time course 12hI-12hNI	1.02788	0.738
Time course 36hI-36hNI	0.82374	0.142
Time course 60hI-60hNI	0.87023	0.081

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)	0.75917	0.348
transgenic ySAMdc/azygous control (breaker)	1.07914	1
transgenic ySAMdc/azygous control (red)	1.00791	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95199	0.404

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.92767	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.95728	1
Manapal/WT (break)	0.71612	0.299
Manapal/WT (red)	0.89314	0.242