Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.4.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8437	0.253
27DAP/17DAP	1.20608	0.836
39DAP/27DAP	1.06481	1
41DAP/39DAP	0.92579	0.678
42DAP/41DAP	1.20306	0.863
43DAP/42DAP	0.93177	0.801
47DAP/43DAP	1.2685	0.542
52DAP/47DAP	0.87132	0.673
57DAP/52DAP	1.51273	0.616

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92388	0.293
17DAP/reference	0.77535	0.008
27DAP/reference	0.99498	0.797
39DAP/reference	0.81542	0.014
41DAP/reference	0.73501	0.008
42DAP/reference	0.98378	0.398
43DAP/reference	0.94428	0.247
47DAP/reference	1.09131	0.627
52DAP/reference	1.33463	0.04
57DAP/reference	1.4002	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.57942	0.699
27DAP/17DAP	0.82751	0.782
39DAP/27DAP	1.19142
41DAP/39DAP	N/A	N/A
42DAP/41DAP	1.15038	1
43DAP/42DAP	N/A	N/A
47DAP/43DAP	0.93682
52DAP/47DAP	0.68479	0.036
57DAP/52DAP	1.14711	0.841
57DAP/7DAP	0.31641	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22121	0.095
17DAP/reference	1.27972	0.038
27DAP/reference	1.00067	0.698
39DAP/reference	1.45605	0.048
41DAP/reference	1.06275	0.314
42DAP/reference	1.26214	0.059
43DAP/reference	1.48337	0.016
47DAP/reference	1.31577	0.099
52DAP/reference	1.21995	0.041
57DAP/reference	1.24635	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.73301	0.164
17DAP/reference	0.67549	0.008
27DAP/reference	0.87182	0.229
39DAP/reference	1.05758	1
41DAP/reference	1.03887	1
42DAP/reference	0.98014	0.534
43DAP/reference	0.69864	0.01
47DAP/reference	0.79882	0.029
52DAP/reference	1.0375	0.988
57DAP/reference	0.82478	0.194

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86433	0.362
17DAP/reference	0.91068	0.249
27DAP/reference	0.9713	0.465
39DAP/reference	1.00462	0.889
41DAP/reference	0.86658	0.132
42DAP/reference	1.20516	0.046
43DAP/reference	1.08744	0.646
47DAP/reference	1.03425	1
52DAP/reference	1.12519	0.542
57DAP/reference	1.76484	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95113	1
26DAP/20DAP	0.95196
34DAP/26DAP	1.24727	0.819
51DAP/34DAP	1.06635	0.883
52DAP/51DAP	1.47381	0.158
53DAP/52DAP	1.27552	0.901
55DAP/53DAP	N/A	N/A
57DAP/55DAP	0.838	0.479
62DAP/57DAP	0.56205	0.002
68DAP/62DAP	7.73061	0.081
68DAP/14DAP	2.52342	0.037

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.77065	0.821

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.37973	0.074
Mature Green Tomato/Ripe Tomato	0.62367	0.033
Immature Eggplant/Mature Eggplant	1.11052	0.348
Ripe Pepper/Ripe Tomato	2.17133	0.256
Mature Eggplant/Ripe Tomato	0.60953	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.83939	0.944
1-1-2/M82	1.13854	1
12-2/M82	0.93475	0.955
12-4/M82	0.74275	0.272
1-3/M82	1.4354	0.248
2-1-1/M82	0.9668	0.465
2-1/M82	0.89238	0.74
2-6/M82	0.9473	1
3-2/M82	1.13316	0.84
4-1-1/M82	1.11981	1
4-1/M82	N/A	N/A
4-3-2/M82	1.05784	1
4-3/M82	1.36236	0.268
5-3/M82	0.94877	1
6-2/M82	0.75638
6-3/M82	N/A	N/A
7-1/M82	0.9122	0.803
7-2/M82	0.9364	0.881
9-3-2/M82	1.31009	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.07151
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.84752	1
IL12-4/WTpooled	0.90242	0.71
IL1-4/WTpooled	1.41751
WT/WTpooled	0.97145	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05127	0.921
DC3000/delta hrp 6h	0.85033	0.95
DC3000/delta hrp 12h	1.14291	1
DC3000/delta hrp 24h	0.73061	0.083

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	1.01529	1
Exp 36h	1.05131	1
Exp 60h	1.18523	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.0338	0.305
transgenic ySAMdc/azygous control (breaker)	1.17102	0.178
transgenic ySAMdc/azygous control (red)	0.88871	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.30185	0.059

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.94709	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.06469	1
Manapal/WT (break)	0.88046	1
Manapal/WT (red)	1.15186	0.413