Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.17.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06675	0.964
27DAP/17DAP	1.40708	0.528
39DAP/27DAP	1.15954	0.787
41DAP/39DAP	0.90804	0.619
42DAP/41DAP	1.07492	0.931
43DAP/42DAP	0.95308	0.892
47DAP/43DAP	0.66308	0.16
52DAP/47DAP	1.60804	0.346
57DAP/52DAP	0.92731	0.92

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23237	0.587
17DAP/reference	0.77242	0.158
27DAP/reference	1.13409	0.277
39DAP/reference	0.91387	0.381
41DAP/reference	0.90465	0.341
42DAP/reference	1.0848	0.299
43DAP/reference	0.96756	0.675
47DAP/reference	1.11486	0.379
52DAP/reference	1.24498	0.018
57DAP/reference	1.31193	0.097

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.39591	0.189
27DAP/17DAP	0.84675	0.508
39DAP/27DAP	1.15002	0.418
41DAP/39DAP	1.13796	0.753
42DAP/41DAP	1.16696	0.622
43DAP/42DAP	1.03752	0.83
47DAP/43DAP	1.12504	0.52
52DAP/47DAP	0.90299	0.612
57DAP/52DAP	1.19372	0.417
57DAP/7DAP	1.71146	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09941	0.732
17DAP/reference	0.85434	0.22
27DAP/reference	0.89205	0.125
39DAP/reference	1.00559	0.745
41DAP/reference	0.89175	0.203
42DAP/reference	0.85725	0.09
43DAP/reference	1.02662	0.802
47DAP/reference	1.02044	0.915
52DAP/reference	1.04559	0.781
57DAP/reference	0.98434	0.477

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93718	0.607
17DAP/reference	1.01962	0.711
27DAP/reference	0.96971	0.537
39DAP/reference	1.88565	0.034
41DAP/reference	1.12415	1
42DAP/reference	1.19553	0.153
43DAP/reference	0.87135	0.257
47DAP/reference	1.1036	0.572
52DAP/reference	1.26828	0.223
57DAP/reference	1.02236	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02772	1
17DAP/reference	0.8342	0.231
27DAP/reference	0.85689	0.218
39DAP/reference	0.91738	0.111
41DAP/reference	0.96384	0.512
42DAP/reference	0.98624	0.816
43DAP/reference	1.15941	0.264
47DAP/reference	1.05559	0.877
52DAP/reference	0.88339	0.415
57DAP/reference	0.86379	0.273

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.88395	1
26DAP/20DAP	1.29884	0.172
34DAP/26DAP	0.9504	0.917
51DAP/34DAP	1.39956	0.032
52DAP/51DAP	0.98577	1
53DAP/52DAP	1.23174	0.623
55DAP/53DAP	0.59392	0.034
57DAP/55DAP	1.28532	0.51
62DAP/57DAP	0.98997	1
68DAP/62DAP	0.714	0.609
68DAP/14DAP	0.8042	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.0703	0.7

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.03913
Mature Green Tomato/Ripe Tomato	1.86385	0.331
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.25482
Mature Eggplant/Ripe Tomato	1.62489	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09993	1
1-1-2/M82	1.06291
12-2/M82	N/A	N/A
12-4/M82	0.84495	0.257
1-3/M82	1.75039
2-1-1/M82	0.57635
2-1/M82	1.2549
2-6/M82	N/A	N/A
3-2/M82	0.90657
4-1-1/M82	0.80533
4-1/M82	N/A	N/A
4-3-2/M82	0.71574	0.698
4-3/M82	1.12136	1
5-3/M82	1.13006	1
6-2/M82	0.92868
6-3/M82	1.21367	1
7-1/M82	1.09107
7-2/M82	0.82413	0.599
9-3-2/M82	0.83346	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.46101	0.243
IL2-6/WTpooled	2.47318	0.395
IL7-5/WTpooled	1.02454	1
IL7-3/WTpooled	0.58952	0.294
IL12-4/WTpooled	1.83372	0.785
IL1-4/WTpooled	1.88641	1
WT/WTpooled	1.10509	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	1.58379	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9337	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.79085
DC3000/delta hrp 24h	1.33048	0.062

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.57609
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	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	1.0419	1
Var 0h	0.83119	0.457
Var 12h I row2-row1	1.15009	0.443
Var 12h NI row2-row1	1.31635	0.266
Var 36h I row2-row1	0.99968	1
Var 36h NI row2-row1	0.90751	0.61
Var 60h I row2-row1	0.96481	0.832
Var 60h NI row2-row1	0.95956	1
Time course 0hI-0hNI	0.95084	0.751
Time course 12hI-12hNI	1.03933	0.72
Time course 36hI-36hNI	1.58707	0.005
Time course 60hI-60hNI	2.10326	0.008

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)	0.88052	0.567
transgenic ySAMdc/azygous control (breaker)	1.08621	1
transgenic ySAMdc/azygous control (red)	0.84523	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.59425	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.01984	1
Manapal/WT (red)	1.39277	0.164