Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.10.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.23016	0.725
27DAP/17DAP	0.92551	0.851
39DAP/27DAP	0.63904	0.301
41DAP/39DAP	1.00697	0.894
42DAP/41DAP	0.67617	0.774
43DAP/42DAP	0.97935	0.925
47DAP/43DAP	0.8541	0.546
52DAP/47DAP	1.38599	0.52
57DAP/52DAP	0.77323	0.622

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87672	0.136
17DAP/reference	0.80836	0.007
27DAP/reference	0.76427	0.013
39DAP/reference	0.79047	0.078
41DAP/reference	0.78628	0.031
42DAP/reference	0.84781	0.015
43DAP/reference	0.80448	0.043
47DAP/reference	0.79924	0.001
52DAP/reference	0.80058	0.06
57DAP/reference	0.91362	0.017

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84836	0.112
27DAP/17DAP	0.91758	0.748
39DAP/27DAP	0.85933	0.361
41DAP/39DAP	0.94722	0.849
42DAP/41DAP	1.07116	0.904
43DAP/42DAP	0.67956	0.045
47DAP/43DAP	0.85651	0.305
52DAP/47DAP	1.40626	0.343
57DAP/52DAP	1.36541	0.097
57DAP/7DAP	0.89704	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86504	0.138
17DAP/reference	0.89538	0.108
27DAP/reference	0.96382	0.303
39DAP/reference	0.59327	0.011
41DAP/reference	0.74753	0.03
42DAP/reference	0.72574	0.015
43DAP/reference	0.81545	0.091
47DAP/reference	0.78822	0.066
52DAP/reference	0.77462	0.072
57DAP/reference	0.62704	0.022

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85184	0.17
17DAP/reference	0.8169	0.009
27DAP/reference	0.94296	0.366
39DAP/reference	0.92823	0.083
41DAP/reference	0.85204	0.096
42DAP/reference	0.85974	0.028
43DAP/reference	1.00984	0.801
47DAP/reference	0.83578	0.035
52DAP/reference	0.78055	0.01
57DAP/reference	0.82932	0.014

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15659	0.167
17DAP/reference	1.09973	0.253
27DAP/reference	1.04227	0.777
39DAP/reference	0.95418	0.36
41DAP/reference	1.17175	0.15
42DAP/reference	1.04942	0.701
43DAP/reference	0.86789	0.158
47DAP/reference	0.93996	0.371
52DAP/reference	0.81194	0.141
57DAP/reference	1.08827	0.57

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.52898	0.966
26DAP/20DAP	1.10045	1
34DAP/26DAP	1.87344	0.542
51DAP/34DAP	0.8351
52DAP/51DAP	0.94747	1
53DAP/52DAP	0.96637	0.876
55DAP/53DAP	1.04357	0.939
57DAP/55DAP	1.20142	0.906
62DAP/57DAP	1.24273	0.868
68DAP/62DAP	1.19429	0.831
68DAP/14DAP	1.33377	0.419

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.68879	0.108

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.66706	0.208
Mature Green Tomato/Ripe Tomato	3.8691	0.015
Immature Eggplant/Mature Eggplant	0.80649	0.089
Ripe Pepper/Ripe Tomato	2.52017
Mature Eggplant/Ripe Tomato	3.59937

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.85591
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.85231
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.01458
7-2/M82	N/A	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	1.27052
IL2-6/WTpooled	1.03724	1
IL7-5/WTpooled	0.82031	1
IL7-3/WTpooled	0.75071	0.418
IL12-4/WTpooled	1.1469
IL1-4/WTpooled	1.08357	1
WT/WTpooled	0.92311	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	1.02075	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.78904	0.839
DC3000/delta hrp 6h	1.00042	0.95
DC3000/delta hrp 12h	1.00336	1
DC3000/delta hrp 24h	0.72379	0.038

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.68209	0.047
DC3000 delta B/DC3000 delta AB	0.71144	0.056

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.82913	1
Exp 36h	0.78899	0.456
Exp 60h	0.67244	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97758	1
Var 0h	0.63928	0.933
Var 12h I row2-row1	0.96112	0.338
Var 12h NI row2-row1	0.86369	0.443
Var 36h I row2-row1	1.01379	1
Var 36h NI row2-row1	1.15003	1
Var 60h I row2-row1	0.99701	1
Var 60h NI row2-row1	1.01935	1
Time course 0hI-0hNI	0.90338	0.185
Time course 12hI-12hNI	0.92773	0.089
Time course 36hI-36hNI	0.75725	0.041
Time course 60hI-60hNI	0.19685	0.005

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)	1.26112	0.246
transgenic ySAMdc/azygous control (breaker)	0.95058	1
transgenic ySAMdc/azygous control (red)	1.05526	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.84101	0.077

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.52692	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.66	0.083
Manapal/WT (break)	2.80412	0.14
Manapal/WT (red)	3.56924	0.15