Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.15.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04274	0.961
27DAP/17DAP	1.03832	0.895
39DAP/27DAP	0.7986	0.462
41DAP/39DAP	1.47022	0.172
42DAP/41DAP	0.932	1
43DAP/42DAP	0.92716	0.801
47DAP/43DAP	1.28674	0.258
52DAP/47DAP	0.94922	0.812
57DAP/52DAP	0.88587	0.759

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88864	0.089
17DAP/reference	0.89017	0.208
27DAP/reference	1.01776	0.806
39DAP/reference	0.98524	0.762
41DAP/reference	0.8328	0.026
42DAP/reference	0.93041	0.059
43DAP/reference	0.90485	0.093
47DAP/reference	0.97503	0.392
52DAP/reference	0.98728	0.598
57DAP/reference	1.13911	0.063

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9131	0.311
27DAP/17DAP	0.96611	0.724
39DAP/27DAP	1.06081	0.581
41DAP/39DAP	1.14596	0.868
42DAP/41DAP	0.96671	0.721
43DAP/42DAP	1.03254	0.664
47DAP/43DAP	0.96249	0.805
52DAP/47DAP	0.97531	0.893
57DAP/52DAP	1.01884	0.992
57DAP/7DAP	1.0233	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97833	0.55
17DAP/reference	0.98439	0.518
27DAP/reference	0.99569	0.698
39DAP/reference	1.03887	0.779
41DAP/reference	1.04684	0.507
42DAP/reference	1.03735	0.889
43DAP/reference	1.04378	0.672
47DAP/reference	1.00985	0.932
52DAP/reference	0.93747	0.196
57DAP/reference	1.08733	0.308

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95434	0.399
17DAP/reference	0.8441	0.007
27DAP/reference	0.83544	0.049
39DAP/reference	0.81425	0.06
41DAP/reference	0.98624	0.519
42DAP/reference	0.87601	0.046
43DAP/reference	0.87927	0.135
47DAP/reference	0.89628	0.032
52DAP/reference	0.92149	0.017
57DAP/reference	0.80822	0.011

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06777	0.408
17DAP/reference	1.00342	0.87
27DAP/reference	1.14759	0.1
39DAP/reference	1.03376	0.792
41DAP/reference	0.97783	0.56
42DAP/reference	1.07386	0.556
43DAP/reference	0.96153	0.305
47DAP/reference	1.01064	1
52DAP/reference	0.98627	0.732
57DAP/reference	1.12649	0.378

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03748	0.966
26DAP/20DAP	0.86998	0.512
34DAP/26DAP	1.01774	1
51DAP/34DAP	0.94833	0.606
52DAP/51DAP	0.96755	1
53DAP/52DAP	0.93412	0.684
55DAP/53DAP	0.97054	0.775
57DAP/55DAP	1.00776	1
62DAP/57DAP	1.14013	0.678
68DAP/62DAP	1.03108	0.95
68DAP/14DAP	1.23575	0.558

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.73044	0.059

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.02568	1
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.6726
Mature Eggplant/Ripe Tomato	1.03912

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99931	1
1-1-2/M82	0.83971
12-2/M82	N/A	N/A
12-4/M82	0.94107	1
1-3/M82	0.80407	0.378
2-1-1/M82	1.01409	1
2-1/M82	N/A	N/A
2-6/M82	1.27728	0.374
3-2/M82	0.78294	1
4-1-1/M82	0.95703	1
4-1/M82	0.92382	1
4-3-2/M82	0.92126
4-3/M82	0.76505	0.72
5-3/M82	0.92523	0.642
6-2/M82	N/A	N/A
6-3/M82	1.12392	1
7-1/M82	N/A	N/A
7-2/M82	1.02526	1
9-3-2/M82	0.89482

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.90859	0.321
IL2-6/WTpooled	1.15178	0.392
IL7-5/WTpooled	0.61296	1
IL7-3/WTpooled	1.03797	1
IL12-4/WTpooled	1.28475	0.481
IL1-4/WTpooled	0.86375	0.699
WT/WTpooled	1.01758	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	0.70929

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95066	0.941
DC3000/delta hrp 6h	1.46464	1
DC3000/delta hrp 12h	1.08347	1
DC3000/delta hrp 24h	1.12433	0.347

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.77707	0.124
DC3000 delta B/DC3000 delta AB	0.95184	0.638

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02678	1
Exp 36h	1.19612	1
Exp 60h	1.09556	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98988	1
Var 0h	0.97309	0.98
Var 12h I row2-row1	1.07416	0.58
Var 12h NI row2-row1	0.9994	1
Var 36h I row2-row1	0.94968	1
Var 36h NI row2-row1	0.94999	0.743
Var 60h I row2-row1	1.2175	0.562
Var 60h NI row2-row1	1.28531	0.904
Time course 0hI-0hNI	1.14029	0.662
Time course 12hI-12hNI	1.08182	0.611
Time course 36hI-36hNI	0.94777	0.269
Time course 60hI-60hNI	1.18652	0.096

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)	1.06941	0.325
transgenic ySAMdc/azygous control (breaker)	0.9966	1
transgenic ySAMdc/azygous control (red)	0.96277	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99881	0.911

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.06303	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.96815	1
Manapal/WT (break)	1.01279	1
Manapal/WT (red)	0.86609	0.607