Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.13.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98038	0.83
27DAP/17DAP	1.0052	1
39DAP/27DAP	1.20749	0.425
41DAP/39DAP	1.06744	0.701
42DAP/41DAP	1.08701	0.888
43DAP/42DAP	1.02074	0.937
47DAP/43DAP	0.87842	0.603
52DAP/47DAP	1.01496	0.976
57DAP/52DAP	1.03836	0.941

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9803	0.476
17DAP/reference	1.00234	1
27DAP/reference	0.96524	0.514
39DAP/reference	1.03104	0.224
41DAP/reference	1.04157	0.265
42DAP/reference	0.95538	0.067
43DAP/reference	0.97196	0.631
47DAP/reference	0.94522	0.098
52DAP/reference	0.96067	0.489
57DAP/reference	1.01822	0.984

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97386	0.613
27DAP/17DAP	0.99749	0.969
39DAP/27DAP	0.98599	0.932
41DAP/39DAP	1.04234	0.719
42DAP/41DAP	0.98269	0.787
43DAP/42DAP	1.0004	1
47DAP/43DAP	0.99725	0.997
52DAP/47DAP	0.98598	0.919
57DAP/52DAP	0.98951	0.823
57DAP/7DAP	1.01877	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97906	0.55
17DAP/reference	0.95062	0.012
27DAP/reference	0.9295
39DAP/reference	0.99666	0.745
41DAP/reference	0.91907	0.023
42DAP/reference	0.98979	0.612
43DAP/reference	0.97579	0.459
47DAP/reference	1.1072	0.112
52DAP/reference	0.88883	0.012
57DAP/reference	0.90139	0.149

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01309	0.842
17DAP/reference	0.98289	0.576
27DAP/reference	0.91924	0.188
39DAP/reference	0.89531	0.062
41DAP/reference	0.89646	0.091
42DAP/reference	1.00861	1
43DAP/reference	0.96004	0.486
47DAP/reference	1.04721	0.482
52DAP/reference	0.92371	0.031
57DAP/reference	1.00795	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99731	0.804
17DAP/reference	0.92541	0.444
27DAP/reference	0.94723	0.184
39DAP/reference	0.8635
41DAP/reference	0.90305	0.185
42DAP/reference	0.88805	0.172
43DAP/reference	0.88902	0.246
47DAP/reference	0.95372	0.296
52DAP/reference	0.99409	0.888
57DAP/reference	0.79056	0.022

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04575	0.966
26DAP/20DAP	1.017	1
34DAP/26DAP	1.06125	0.542
51DAP/34DAP	0.97255	0.758
52DAP/51DAP	0.99017	1
53DAP/52DAP	0.97121	0.897
55DAP/53DAP	1.17794	0.164
57DAP/55DAP	0.9455	0.783
62DAP/57DAP	0.94878	0.681
68DAP/62DAP	1.03314	0.977
68DAP/14DAP	1.06661	0.656

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.94058	0.358

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.25738	0.176
Mature Green Tomato/Ripe Tomato	1.13865	0.523
Immature Eggplant/Mature Eggplant	10.251	0.05
Ripe Pepper/Ripe Tomato	0.24771	0.224
Mature Eggplant/Ripe Tomato	1.07344	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.89798	0.907
1-1-2/M82	0.97062	0.958
12-2/M82	0.97164	0.955
12-4/M82	0.98268	0.619
1-3/M82	0.98925	1
2-1-1/M82	0.92001	0.465
2-1/M82	1.09734	0.345
2-6/M82	0.95911	1
3-2/M82	0.99822	1
4-1-1/M82	1.04411	1
4-1/M82	0.93708	1
4-3-2/M82	1.25141	0.262
4-3/M82	0.94899	0.72
5-3/M82	0.9685	1
6-2/M82	1.00179	1
6-3/M82	0.95472	1
7-1/M82	0.97193	1
7-2/M82	0.98248	1
9-3-2/M82	1.02178	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.21461	0.419
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.16284	1
IL12-4/WTpooled	1.33295	0.523
IL1-4/WTpooled	0.86933	0.834
WT/WTpooled	0.93853	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	1.90098	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04822	0.921
DC3000/delta hrp 6h	1.15657	1
DC3000/delta hrp 12h	0.96431	1
DC3000/delta hrp 24h	1.16021	0.347

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.40421	0.045
DC3000 delta B/DC3000 delta AB	1.25317	0.167

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.42238	0.254
Exp 36h	1.69877	0.489
Exp 60h	2.12016	0.221

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98209	1
Var 0h	1.03924	0.98
Var 12h I row2-row1	1.517	0.506
Var 12h NI row2-row1	1.05276	0.649
Var 36h I row2-row1	1.09906	0.489
Var 36h NI row2-row1	0.93342	0.645
Var 60h I row2-row1	1.0825	1
Var 60h NI row2-row1	1.07166	1
Time course 0hI-0hNI	1.05749	0.852
Time course 12hI-12hNI	1.07946	0.512
Time course 36hI-36hNI	1.45016	0.005
Time course 60hI-60hNI	1.99059	0.009

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)	0.78843	0.291
transgenic ySAMdc/azygous control (breaker)	0.69551	0.251
transgenic ySAMdc/azygous control (red)	1.34754	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9514	0.104

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.83061	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.34143	0.307
Manapal/WT (break)	0.53546	0.299
Manapal/WT (red)	1.10576	1