Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-2.3.15.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.76142	0.169
27DAP/17DAP	0.95174	0.908
39DAP/27DAP	0.93835	0.529
41DAP/39DAP	1.11004	0.735
42DAP/41DAP	0.84461	0.774
43DAP/42DAP	0.94158	0.834
47DAP/43DAP	0.8064	0.424
52DAP/47DAP	1.08481	0.906
57DAP/52DAP	1.04413	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82826	0.077
17DAP/reference	1.19206	0.248
27DAP/reference	1.51923	0.021
39DAP/reference	1.16298	0.144
41DAP/reference	1.03838	1
42DAP/reference	0.89753	0.013
43DAP/reference	0.97436	0.611
47DAP/reference	1.01729	1
52DAP/reference	1.14694	0.32
57DAP/reference	1.26764	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.71292	0.065
27DAP/17DAP	1.05085	0.988
39DAP/27DAP	1.02572	1
41DAP/39DAP	1.11607	0.304
42DAP/41DAP	0.82766	0.339
43DAP/42DAP	1.01313	0.83
47DAP/43DAP	0.91643	0.833
52DAP/47DAP	1.24832	0.444
57DAP/52DAP	0.9773	0.789
57DAP/7DAP	1.16825	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84541	0.069
17DAP/reference	1.00463	0.599
27DAP/reference	0.99841	0.698
39DAP/reference	0.91293	0.083
41DAP/reference	1.06359	0.701
42DAP/reference	0.88885	0.095
43DAP/reference	0.96996	0.421
47DAP/reference	0.99055	0.671
52DAP/reference	0.87557	0.196
57DAP/reference	0.79407	0.025

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89747	0.257
17DAP/reference	1.66294	0.008
27DAP/reference	1.35154	0.022
39DAP/reference	1.34451	0.016
41DAP/reference	1.02988	0.981
42DAP/reference	1.03897	0.826
43DAP/reference	1.25399	0.082
47DAP/reference	1.10003	0.301
52DAP/reference	1.3048	0.007
57DAP/reference	0.81102	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00008	0.804
17DAP/reference	1.02933	0.814
27DAP/reference	1.0851	0.596
39DAP/reference	0.97956	0.591
41DAP/reference	0.79662	0.04
42DAP/reference	0.95718	0.361
43DAP/reference	0.90671	0.116
47DAP/reference	0.81532	0.006
52DAP/reference	0.64946	0.052
57DAP/reference	0.99587	0.704

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93088	1
26DAP/20DAP	1.14634	0.931
34DAP/26DAP	1.49022	1
51DAP/34DAP	0.86183	0.522
52DAP/51DAP	0.91639	1
53DAP/52DAP	1.17518	0.108
55DAP/53DAP	1.16804	0.898
57DAP/55DAP	0.82225	0.297
62DAP/57DAP	0.94587	0.871
68DAP/62DAP	1.05161	0.914
68DAP/14DAP	0.90322	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.63263	0.079

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	3.75316	0.267
Immature Eggplant/Mature Eggplant	1.43186	0.165
Ripe Pepper/Ripe Tomato	0.7843	N/A
Mature Eggplant/Ripe Tomato	4.20185	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.22941	0.877
1-1-2/M82	1.01123	1
12-2/M82	N/A	N/A
12-4/M82	0.84789	N/A
1-3/M82	0.70294	N/A
2-1-1/M82	0.72012	0.465
2-1/M82	1.83485	N/A
2-6/M82	0.88081	1
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.26113	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.88621	N/A
6-2/M82	0.81332	1
6-3/M82	1.33003	1
7-1/M82	0.95129	N/A
7-2/M82	0.90631	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.90811	0.321
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.73704	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.0698	N/A
IL1-4/WTpooled	1.07056	1
WT/WTpooled	1.07349	N/A

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	1.06891	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98725	1
DC3000/delta hrp 6h	1.05323	1
DC3000/delta hrp 12h	0.98967	1
DC3000/delta hrp 24h	1.12474	0.453

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.55794	N/A
DC3000 delta B/DC3000 delta AB	0.78925	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0174	1
Exp 36h	0.41557	0.419
Exp 60h	0.60761	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96822	1
Var 0h	1.11161	0.936
Var 12h I row2-row1	1.29882	0.58
Var 12h NI row2-row1	1.0161	1
Var 36h I row2-row1	1.13069	1
Var 36h NI row2-row1	1.13607	1
Var 60h I row2-row1	0.9324	0.952
Var 60h NI row2-row1	0.93515	0.756
Time course 0hI-0hNI	0.91411	0.401
Time course 12hI-12hNI	0.90747	0.592
Time course 36hI-36hNI	0.7719	0.096
Time course 60hI-60hNI	0.60088	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)	1.03394	0.748
transgenic ySAMdc/azygous control (breaker)	0.94857	1
transgenic ySAMdc/azygous control (red)	0.98465	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.24208	0.046

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.94312	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.57425	0.172
Manapal/WT (break)	0.46375	0.299
Manapal/WT (red)	0.73373	0.184