Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.2.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.193	0.755
27DAP/17DAP	1.21109	0.793
39DAP/27DAP	0.92242	0.564
41DAP/39DAP	0.96085	0.772
42DAP/41DAP	0.92003	1
43DAP/42DAP	0.96385	0.91
47DAP/43DAP	1.14328	0.513
52DAP/47DAP	1.08122	0.948
57DAP/52DAP	0.95182	0.952

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10801	0.303
17DAP/reference	0.95444	0.393
27DAP/reference	1.01637	1
39DAP/reference	1.20166	0.021
41DAP/reference	1.05518	0.122
42DAP/reference	1.00679	0.665
43DAP/reference	0.94975	0.302
47DAP/reference	1.06162	0.19
52DAP/reference	1.03019	0.878
57DAP/reference	1.05035	0.621

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97381	0.75
27DAP/17DAP	1.22201	0.798
39DAP/27DAP	1.23144	0.403
41DAP/39DAP	0.91233	0.764
42DAP/41DAP	1.02907	0.823
43DAP/42DAP	1.08287	0.297
47DAP/43DAP	1.00191	0.947
52DAP/47DAP	0.96011	0.884
57DAP/52DAP	1.11728	0.906
57DAP/7DAP	1.20937

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75763	0.104
17DAP/reference	0.94892	0.22
27DAP/reference	1.31937	0.008
39DAP/reference	0.81477	0.027
41DAP/reference	0.92506	0.194
42DAP/reference	1.24175	0.076
43DAP/reference	0.94944	0.279
47DAP/reference	0.91637	0.293
52DAP/reference	0.88045	0.072
57DAP/reference	0.89847	0.132

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32792	0.33
17DAP/reference	1.16773	0.066
27DAP/reference	1.27966	0.089
39DAP/reference	1.09292	0.401
41DAP/reference	1.11844	0.394
42DAP/reference	1.42233	0.009
43DAP/reference	1.70972	0.032
47DAP/reference	1.37631	0.02
52DAP/reference	1.3988	0.012
57DAP/reference	1.25441	0.108

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80882	0.071
17DAP/reference	1.2366	0.283
27DAP/reference	1.03628	0.672
39DAP/reference	1.01108	1
41DAP/reference	1.35367	0.239
42DAP/reference	1.26746	0.027
43DAP/reference	0.9362	0.449
47DAP/reference	1.25551	0.009
52DAP/reference	0.95922	0.562
57DAP/reference	1.22292	0.104

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.20529	0.916
26DAP/20DAP	0.5559
34DAP/26DAP	0.68875	0.666
51DAP/34DAP	0.87809
52DAP/51DAP	0.84755	1
53DAP/52DAP	1.01091	1
55DAP/53DAP	1.0451	0.876
57DAP/55DAP	0.62376	0.09
62DAP/57DAP	0.93996
68DAP/62DAP	1.42843	0.597
68DAP/14DAP	0.98468	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.69931	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.9639	0.715
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.24177	0.224
Mature Eggplant/Ripe Tomato	0.15307

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.22435	0.742
1-1-2/M82	1.18148	1
12-2/M82	1.76027
12-4/M82	1.32606	0.599
1-3/M82	0.72447	0.501
2-1-1/M82	0.80445
2-1/M82	N/A	N/A
2-6/M82	0.87362	1
3-2/M82	0.71261
4-1-1/M82	N/A	N/A
4-1/M82	1.65395
4-3-2/M82	0.89834
4-3/M82	0.85905	1
5-3/M82	0.8978	1
6-2/M82	0.61116
6-3/M82	1.14416	1
7-1/M82	N/A	N/A
7-2/M82	0.7377
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.5147	1
IL2-6/WTpooled	1.06998	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.20398	0.362
IL12-4/WTpooled	1.09927	0.557
IL1-4/WTpooled	0.83397	0.834
WT/WTpooled	1.00392	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	0.93086	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.10168	0.692
DC3000/delta hrp 6h	1.80365	0.857
DC3000/delta hrp 12h	1.06549	1
DC3000/delta hrp 24h	0.99342	0.988

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.11479	1
Exp 36h	1.15478	1
Exp 60h	1.23391	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	1.20422
Var 0h	1.14654	0.98
Var 12h I row2-row1	1.21374	0.443
Var 12h NI row2-row1	0.95511	0.82
Var 36h I row2-row1	0.9155	1
Var 36h NI row2-row1	1.08789	1
Var 60h I row2-row1	0.83653	0.292
Var 60h NI row2-row1	0.4933	0.516
Time course 0hI-0hNI	1.07372	0.799
Time course 12hI-12hNI	1.24583	0.367
Time course 36hI-36hNI	1.01613	1
Time course 60hI-60hNI	1.07603	0.495

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)	0.90831	0.229
transgenic ySAMdc/azygous control (breaker)	1.98056	0.162
transgenic ySAMdc/azygous control (red)	1.05274	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00647	0.687

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.87201	1
Manapal/WT (break)	0.85335	0.333
Manapal/WT (red)	0.78593	0.229