Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.6.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1273	0.615
27DAP/17DAP	1.39904	0.625
39DAP/27DAP	0.80331	0.462
41DAP/39DAP	1.20428	0.37
42DAP/41DAP	0.88319	1
43DAP/42DAP	1.27055	0.698
47DAP/43DAP	1.16295	0.474
52DAP/47DAP	0.73921	0.32
57DAP/52DAP	1.07777	0.955

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10757	0.154
17DAP/reference	1.01987	0.606
27DAP/reference	1.04258	0.426
39DAP/reference	0.97314	0.651
41DAP/reference	1.05265	0.111
42DAP/reference	1.13608	0.007
43DAP/reference	1.01366	0.982
47DAP/reference	1.10971	0.009
52DAP/reference	1.19199	0.134
57DAP/reference	1.01029	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96294	0.644
27DAP/17DAP	1.02224	0.957
39DAP/27DAP	1.15496	0.241
41DAP/39DAP	1.04283	1
42DAP/41DAP	0.98817	0.83
43DAP/42DAP	1.12481	0.478
47DAP/43DAP	1.00544	1
52DAP/47DAP	0.99193	0.947
57DAP/52DAP	0.95029	0.384
57DAP/7DAP	1.00256	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.55617	0.085
17DAP/reference	1.27508	0.147
27DAP/reference	0.89367	0.231
39DAP/reference	1.15487	0.252
41DAP/reference	0.94397	0.357
42DAP/reference	1.10981	0.889
43DAP/reference	0.98473	0.555
47DAP/reference	0.97151	0.504
52DAP/reference	0.97859	0.477
57DAP/reference	1.27879	0.158

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11599	0.193
17DAP/reference	1.19902	0.032
27DAP/reference	1.20379	0.153
39DAP/reference	1.19379	0.175
41DAP/reference	1.12928	0.471
42DAP/reference	1.12996	0.22
43DAP/reference	1.21775	0.137
47DAP/reference	1.06225	0.164
52DAP/reference	1.11896	0.024
57DAP/reference	1.1315	0.104

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16024	0.347
17DAP/reference	1.13128	0.362
27DAP/reference	0.9079
39DAP/reference	1.07473	0.175
41DAP/reference	1.16108	0.306
42DAP/reference	1.41601	0.056
43DAP/reference	1.19144	0.246
47DAP/reference	1.05067	0.207
52DAP/reference	1.0783	0.779
57DAP/reference	1.15144	0.184

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99408	1
26DAP/20DAP	0.91533	1
34DAP/26DAP	1.07925	0.819
51DAP/34DAP	0.82458	0.121
52DAP/51DAP	0.99674	1
53DAP/52DAP	1.05073	0.819
55DAP/53DAP	1.03869	0.869
57DAP/55DAP	1.02528	0.955
62DAP/57DAP	1.14026	0.257
68DAP/62DAP	0.70599	0.505
68DAP/14DAP	1.13357	0.436

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.98577	0.665

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.65621	0.232
Mature Green Tomato/Ripe Tomato	1.05419	0.948
Immature Eggplant/Mature Eggplant	1.65621	0.05
Ripe Pepper/Ripe Tomato	0.82643	1
Mature Eggplant/Ripe Tomato	1.05503	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97103	0.944
1-1-2/M82	0.87659	0.958
12-2/M82	0.96913
12-4/M82	0.86423	0.358
1-3/M82	0.92542	0.378
2-1-1/M82	0.94847	1
2-1/M82	N/A	N/A
2-6/M82	0.96612	0.421
3-2/M82	0.91035	1
4-1-1/M82	0.99732	1
4-1/M82	0.99259	1
4-3-2/M82	0.86745	0.698
4-3/M82	1.04934	1
5-3/M82	0.91629	0.364
6-2/M82	0.79627
6-3/M82	1.08436
7-1/M82	0.9559
7-2/M82	0.84698
9-3-2/M82	0.83077	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.77156
IL12-4/WTpooled	0.85969	0.581
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	0.95552	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	0.85851	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00109	1
DC3000/delta hrp 6h	1.18894	1
DC3000/delta hrp 12h	1.089	1
DC3000/delta hrp 24h	1.05965	0.502

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.12757	0.042
DC3000 delta B/DC3000 delta AB	1.04531	0.51

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	0.8573	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	0.93918
Var 0h	0.75379	0.933
Var 12h I row2-row1	1.00425	0.795
Var 12h NI row2-row1	0.89184	0.466
Var 36h I row2-row1	0.7811	1
Var 36h NI row2-row1	0.98397	0.791
Var 60h I row2-row1	1.10375	0.543
Var 60h NI row2-row1	1.10051	0.904
Time course 0hI-0hNI	1.27999	0.603
Time course 12hI-12hNI	0.98965	0.972
Time course 36hI-36hNI	0.93073	0.265
Time course 60hI-60hNI	1.07915	0.025

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)	1.04801	0.347
transgenic ySAMdc/azygous control (breaker)	1.0334	1
transgenic ySAMdc/azygous control (red)	1.0754	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96563	0.115

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.83954	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.21283	0.096
Manapal/WT (break)	1.11545	1
Manapal/WT (red)	1.23314	0.222