Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.2.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85158	0.178
27DAP/17DAP	1.17413	0.804
39DAP/27DAP	1.2315	0.631
41DAP/39DAP	1.05798	1
42DAP/41DAP	1.28009	0.632
43DAP/42DAP	1.16169	1
47DAP/43DAP	0.84426	0.517
52DAP/47DAP	0.96151	0.786
57DAP/52DAP	1.11064	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94091	0.162
17DAP/reference	1.01977	0.585
27DAP/reference	1.03881	0.457
39DAP/reference	1.00667	0.889
41DAP/reference	0.9883	0.814
42DAP/reference	1.00356	0.731
43DAP/reference	1.02053	0.812
47DAP/reference	0.93014	0.007
52DAP/reference	0.87984	0.06
57DAP/reference	0.97923	0.526

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9946	0.847
27DAP/17DAP	1.05833	0.852
39DAP/27DAP	1.00046	1
41DAP/39DAP	1.20549	0.163
42DAP/41DAP	1.00065	0.876
43DAP/42DAP	1.12559	0.112
47DAP/43DAP	1.04071	0.865
52DAP/47DAP	0.99837	0.962
57DAP/52DAP	0.92656	0.426
57DAP/7DAP	0.94687	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20764	0.16
17DAP/reference	1.33317	0.013
27DAP/reference	1.53884	0.009
39DAP/reference	1.47683	0.016
41DAP/reference	1.4294	0.014
42DAP/reference	1.67372	0.008
43DAP/reference	1.92845	0.007
47DAP/reference	1.36528	0.036
52DAP/reference	1.81349	0.013
57DAP/reference	1.44897	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16061	0.23
17DAP/reference	1.08946	0.101
27DAP/reference	1.1085	0.419
39DAP/reference	1.12626	0.412
41DAP/reference	1.14494	0.157
42DAP/reference	1.01704	1
43DAP/reference	1.04747	0.957
47DAP/reference	0.97867	0.512
52DAP/reference	1.05114	0.559
57DAP/reference	1.15178	0.146

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23987	0.146
17DAP/reference	1.17518	0.258
27DAP/reference	1.45293	0.029
39DAP/reference	1.51763	0.01
41DAP/reference	1.20697	0.065
42DAP/reference	1.24501	0.194
43DAP/reference	1.30983	0.042
47DAP/reference	0.94144	0.224
52DAP/reference	1.56732	0.052
57DAP/reference	1.07064	0.694

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94768	1
26DAP/20DAP	0.90999	1
34DAP/26DAP	0.95505	0.944
51DAP/34DAP	0.91953	0.611
52DAP/51DAP	0.7854	0.079
53DAP/52DAP	0.86906	0.562
55DAP/53DAP	0.92528	0.577
57DAP/55DAP	1.14342	0.826
62DAP/57DAP	1.50552	0.515
68DAP/62DAP	0.92603	0.505
68DAP/14DAP	0.69177	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.844	0.059

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.82721	0.058
Mature Green Tomato/Ripe Tomato	3.23159	0.523
Immature Eggplant/Mature Eggplant	0.84125	0.594
Ripe Pepper/Ripe Tomato	0.78622
Mature Eggplant/Ripe Tomato	0.93892

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.10803
1-1-2/M82	1.09629
12-2/M82	N/A	N/A
12-4/M82	1.25287
1-3/M82	N/A	N/A
2-1-1/M82	0.95003
2-1/M82	N/A	N/A
2-6/M82	0.92594
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.36515
4-3/M82	1.00415	1
5-3/M82	1.22424
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.21027
7-2/M82	1.08368
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.00514
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.63911	0.293
IL12-4/WTpooled	0.85514	0.581
IL1-4/WTpooled	0.95348
WT/WTpooled	0.98895	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	0.92177	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.19511	0.894
DC3000/delta hrp 6h	1.02944	1
DC3000/delta hrp 12h	1.03715	1
DC3000/delta hrp 24h	0.98148	0.851

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.18266	0.384
DC3000 delta B/DC3000 delta AB	0.77999	0.137

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.08736	1
Exp 36h	1.26943	1
Exp 60h	1.22176	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99455	1
Var 0h	0.89137	1
Var 12h I row2-row1	0.83542	0.338
Var 12h NI row2-row1	1.07554	0.34
Var 36h I row2-row1	0.89395	1
Var 36h NI row2-row1	1.17565	1
Var 60h I row2-row1	0.94768	0.952
Var 60h NI row2-row1	0.94543	1
Time course 0hI-0hNI	0.89801	0.254
Time course 12hI-12hNI	0.9826	0.889
Time course 36hI-36hNI	0.9299	0.295
Time course 60hI-60hNI	0.68222	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)	0.94506	0.454
transgenic ySAMdc/azygous control (breaker)	1.16501	0.248
transgenic ySAMdc/azygous control (red)	1.14047	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.014	0.35

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.03539	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.10582	0.307
Manapal/WT (break)	0.81245	0.333
Manapal/WT (red)	1.14676	0.164