Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.15.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11409	0.602
27DAP/17DAP	1.16847	0.833
39DAP/27DAP	0.99298	0.798
41DAP/39DAP	1.22688	0.464
42DAP/41DAP	1.09331	0.978
43DAP/42DAP	0.93899	0.867
47DAP/43DAP	1.07313	0.595
52DAP/47DAP	0.93399	0.793
57DAP/52DAP	1.01284	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93699	0.182
17DAP/reference	0.99041	0.701
27DAP/reference	1.00764	0.925
39DAP/reference	1.00544	0.842
41DAP/reference	0.95042	0.341
42DAP/reference	0.89084	0.015
43DAP/reference	1.02784	0.518
47DAP/reference	0.95515	0.127
52DAP/reference	0.99028	0.598
57DAP/reference	0.90656	0.071

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98304	0.75
27DAP/17DAP	0.95829	0.58
39DAP/27DAP	1.03021	0.742
41DAP/39DAP	0.95529	0.729
42DAP/41DAP	1.03871	0.893
43DAP/42DAP	0.96684	0.351
47DAP/43DAP	0.99345	0.983
52DAP/47DAP	1.01468	0.991
57DAP/52DAP	0.94061	0.476
57DAP/7DAP	0.99589	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98507	0.495
17DAP/reference	1.03619	0.297
27DAP/reference	0.97174	0.325
39DAP/reference	1.01553	0.46
41DAP/reference	0.94296	0.056
42DAP/reference	0.92988	0.055
43DAP/reference	0.97128	0.334
47DAP/reference	1.02243	0.932
52DAP/reference	0.90186	0.106
57DAP/reference	0.91788	0.223

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98659	0.786
17DAP/reference	0.94017	0.279
27DAP/reference	0.90772	0.167
39DAP/reference	0.90523	0.016
41DAP/reference	0.86217	0.051
42DAP/reference	0.91705	0.05
43DAP/reference	1.00414	1
47DAP/reference	0.93284	0.061
52DAP/reference	0.94771	0.101
57DAP/reference	1.06443	0.229

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9704	0.169
17DAP/reference	0.98325	0.709
27DAP/reference	0.96919	0.416
39DAP/reference	1.02562	0.496
41DAP/reference	0.97683	0.56
42DAP/reference	0.90681	0.108
43DAP/reference	0.96678	0.503
47DAP/reference	0.9944	0.667
52DAP/reference	1.04818	0.592
57DAP/reference	0.89644	0.098

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91227	0.672
26DAP/20DAP	0.98341	1
34DAP/26DAP	0.90557	0.741
51DAP/34DAP	1.02234	0.949
52DAP/51DAP	1.11228	0.313
53DAP/52DAP	1.06233	0.83
55DAP/53DAP	0.94322	0.746
57DAP/55DAP	1.17608	0.898
62DAP/57DAP	1.10135	0.767
68DAP/62DAP	0.91346	0.7
68DAP/14DAP	1.3853	0.279

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.05601	0.591

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.74735	0.29
Mature Green Tomato/Ripe Tomato	1.06288	0.814
Immature Eggplant/Mature Eggplant	1.01798	1
Ripe Pepper/Ripe Tomato	0.36841	0.224
Mature Eggplant/Ripe Tomato	0.56573	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.94629	0.605
1-1-2/M82	1.01229	1
12-2/M82	1.16371	1
12-4/M82	0.92689	1
1-3/M82	0.95557	1
2-1-1/M82	1.21466	0.338
2-1/M82	1.57574
2-6/M82	1.02771	0.452
3-2/M82	N/A	N/A
4-1-1/M82	1.10153	0.968
4-1/M82	1.02649
4-3-2/M82	0.78048	0.445
4-3/M82	0.81116
5-3/M82	1.02345	1
6-2/M82	0.88494	0.497
6-3/M82	1.02791	1
7-1/M82	0.80686
7-2/M82	0.97382	1
9-3-2/M82	0.88869	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.86142
IL2-6/WTpooled	1.12005	0.584
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.97158	1
IL12-4/WTpooled	1.00827	1
IL1-4/WTpooled	0.84525	0.834
WT/WTpooled	1.03459	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	1.28268	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97313	1
DC3000/delta hrp 6h	1.05218	0.95
DC3000/delta hrp 12h	1.05317	1
DC3000/delta hrp 24h	1.00295	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.14799	0.145
DC3000 delta B/DC3000 delta AB	1.08736	0.381

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.13854	1
Exp 36h	1.09691	1
Exp 60h	1.26434	0.221

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98895	1
Var 0h	0.43143	1
Var 12h I row2-row1	1.10339	0.209
Var 12h NI row2-row1	1.01991	1
Var 36h I row2-row1	0.8691	1
Var 36h NI row2-row1	1.20784	1
Var 60h I row2-row1	1.26828	0.562
Var 60h NI row2-row1	1.10003	0.904
Time course 0hI-0hNI	1.04807	0.833
Time course 12hI-12hNI	1.00589	1
Time course 36hI-36hNI	1.02506	0.881
Time course 60hI-60hNI	1.20951	0.015

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)	0.88891	0.33
transgenic ySAMdc/azygous control (breaker)	0.91002	0.251
transgenic ySAMdc/azygous control (red)	0.95166	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04063	0.115

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.9321	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.37853	0.096
Manapal/WT (break)	1.44309	0.14
Manapal/WT (red)	1.41581	0.137