Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.7.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9667	0.752
27DAP/17DAP	0.93205	0.899
39DAP/27DAP	1.30879	0.618
41DAP/39DAP	0.96996	0.887
42DAP/41DAP	0.92652	1
43DAP/42DAP	0.98421	0.93
47DAP/43DAP	1.19207	0.659
52DAP/47DAP	1.01007	0.933
57DAP/52DAP	1.02909	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03781	0.611
17DAP/reference	1.02365	0.457
27DAP/reference	1.00733	0.966
39DAP/reference	1.01235	0.816
41DAP/reference	0.95928	0.434
42DAP/reference	0.93258	0.033
43DAP/reference	1.02635	0.617
47DAP/reference	0.89045	0.083
52DAP/reference	0.87145	0.069
57DAP/reference	0.89797	0.106

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.38226	0.062
27DAP/17DAP	1.13243	0.617
39DAP/27DAP	1.17605	0.353
41DAP/39DAP	1.04976	0.876
42DAP/41DAP	0.89388	0.343
43DAP/42DAP	0.88525	0.043
47DAP/43DAP	1.03865	0.749
52DAP/47DAP	1.07436	0.779
57DAP/52DAP	1.31162	0.197
57DAP/7DAP	1.25207	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14322	0.185
17DAP/reference	0.90721	0.22
27DAP/reference	1.06745	1
39DAP/reference	1.53243	0.044
41DAP/reference	1.04857	0.767
42DAP/reference	1.15121	0.405
43DAP/reference	1.14747	0.241
47DAP/reference	1.13216	0.582
52DAP/reference	1.30326	0.02
57DAP/reference	1.20153	0.011

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17193	0.36
17DAP/reference	1.02801	0.824
27DAP/reference	1.06116	0.86
39DAP/reference	0.99234	0.586
41DAP/reference	0.94829	0.322
42DAP/reference	1.02347	1
43DAP/reference	1.0788	0.396
47DAP/reference	0.95244	0.194
52DAP/reference	1.00229	0.761
57DAP/reference	1.12929	0.423

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08456	0.207
17DAP/reference	0.90038	0.275
27DAP/reference	0.97832	0.657
39DAP/reference	0.9179	0.393
41DAP/reference	0.89426	0.185
42DAP/reference	0.86304	0.134
43DAP/reference	0.86994	0.12
47DAP/reference	0.95157	0.24
52DAP/reference	1.08744	0.724
57DAP/reference	0.85222	0.221

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01681	0.966
26DAP/20DAP	1.68609	0.116
34DAP/26DAP	1.00338	1
51DAP/34DAP	0.99733	0.883
52DAP/51DAP	0.99742	1
53DAP/52DAP	1.04567	0.858
55DAP/53DAP	1.03433	0.826
57DAP/55DAP	0.81609	0.458
62DAP/57DAP	1.13265	0.393
68DAP/62DAP	1.01577	0.991
68DAP/14DAP	1.13819	0.656

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.23939	0.172

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.81837	0.287
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.46252
Mature Eggplant/Ripe Tomato	0.69932	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.82726	0.56
1-1-2/M82	1.06815	1
12-2/M82	0.96543	0.955
12-4/M82	0.9214	0.619
1-3/M82	N/A	N/A
2-1-1/M82	0.7005
2-1/M82	0.50115
2-6/M82	0.77468	0.313
3-2/M82	0.74133
4-1-1/M82	0.93684	1
4-1/M82	N/A	N/A
4-3-2/M82	0.96894	1
4-3/M82	0.74166	0.611
5-3/M82	1.05833	1
6-2/M82	0.7846
6-3/M82	0.91197	0.982
7-1/M82	1.01476
7-2/M82	0.99201
9-3-2/M82	0.92727	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.68835	0.321
IL2-6/WTpooled	1.58107	0.456
IL7-5/WTpooled	2.24391	1
IL7-3/WTpooled	0.89692	1
IL12-4/WTpooled	1.05585	0.891
IL1-4/WTpooled	1.03217	1
WT/WTpooled	1.10081	0.89

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	0.88119	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94491	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.20434	1
DC3000/delta hrp 24h	0.96504	0.761

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.19034
DC3000 delta B/DC3000 delta AB	1.05978	0.528

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99108	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.10408	0.473
Var 12h NI row2-row1	0.89031	0.82
Var 36h I row2-row1	1.08576	1
Var 36h NI row2-row1	0.8381	1
Var 60h I row2-row1	0.84892	0.439
Var 60h NI row2-row1	0.98441	1
Time course 0hI-0hNI	0.91794	0.433
Time course 12hI-12hNI	0.99703	1
Time course 36hI-36hNI	0.94254	0.295
Time course 60hI-60hNI	0.79756	0.026

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)	1.17195	0.931
transgenic ySAMdc/azygous control (breaker)	1.71088	1
transgenic ySAMdc/azygous control (red)	1.26138	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02703	0.08

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.20626	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.05571	1
Manapal/WT (break)	1.04013	0.183
Manapal/WT (red)	1.3998	0.164