Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.13.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96206	0.743
27DAP/17DAP	1.22275	0.847
39DAP/27DAP	0.89709	0.573
41DAP/39DAP	1.23265	0.37
42DAP/41DAP	0.93847	1
43DAP/42DAP	0.9768	0.925
47DAP/43DAP	0.89909	0.663
52DAP/47DAP	1.30483	0.441
57DAP/52DAP	0.99559	0.982

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97444	0.422
17DAP/reference	0.98224	0.536
27DAP/reference	1.0284	0.509
39DAP/reference	0.99161	0.841
41DAP/reference	1.02341	0.587
42DAP/reference	0.95751	0.151
43DAP/reference	0.98698	0.708
47DAP/reference	0.92929	0.011
52DAP/reference	0.99142	0.618
57DAP/reference	0.92622	0.074

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03933	0.719
27DAP/17DAP	0.98538	0.919
39DAP/27DAP	1.0139	0.751
41DAP/39DAP	1.04952	0.719
42DAP/41DAP	1.02539	0.861
43DAP/42DAP	1.00918	0.746
47DAP/43DAP	1.03142	0.884
52DAP/47DAP	1.04339	0.868
57DAP/52DAP	1.04511	0.718
57DAP/7DAP	1.07167	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93692	0.129
17DAP/reference	1.0217	0.477
27DAP/reference	1.00229	1
39DAP/reference	0.99032	0.552
41DAP/reference	1.01282	0.767
42DAP/reference	1.05242	0.308
43DAP/reference	1.02363	0.307
47DAP/reference	0.95689	0.383
52DAP/reference	0.99498	0.621
57DAP/reference	1.0154	0.851

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00089	0.97
17DAP/reference	1.00348	0.898
27DAP/reference	1.00014	1
39DAP/reference	0.96886	0.314
41DAP/reference	1.05419	0.737
42DAP/reference	0.91009	0.073
43DAP/reference	1.04862	0.704
47DAP/reference	0.95578	0.368
52DAP/reference	0.98469	0.259
57DAP/reference	0.95988	0.278

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93828	0.092
17DAP/reference	0.95401	0.322
27DAP/reference	1.04338	0.284
39DAP/reference	1.03238	0.39
41DAP/reference	0.99951	1
42DAP/reference	0.95006	0.028
43DAP/reference	0.99577	0.796
47DAP/reference	0.89203	0.139
52DAP/reference	1.00491	0.99
57DAP/reference	0.78233	0.078

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02455	0.966
26DAP/20DAP	0.93243	1
34DAP/26DAP	0.93579	0.509
51DAP/34DAP	1.07261	0.706
52DAP/51DAP	1.01763	0.873
53DAP/52DAP	0.91121	0.281
55DAP/53DAP	1.16488	0.229
57DAP/55DAP	0.95524	0.855
62DAP/57DAP	0.99553	1
68DAP/62DAP	1.06128	0.707
68DAP/14DAP	1.15573	0.17

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.03801	0.558

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.29036	0.417
Mature Green Tomato/Ripe Tomato	0.71119	0.148
Immature Eggplant/Mature Eggplant	0.60724
Ripe Pepper/Ripe Tomato	0.18644	0.224
Mature Eggplant/Ripe Tomato	0.20773	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97787	0.944
1-1-2/M82	0.80849	1
12-2/M82	1.00319	1
12-4/M82	0.92745	1
1-3/M82	0.93125	0.351
2-1-1/M82	1.09161	1
2-1/M82	N/A	N/A
2-6/M82	0.92021	1
3-2/M82	1.04739	0.717
4-1-1/M82	1.02107	1
4-1/M82	0.99138	1
4-3-2/M82	0.89884	0.698
4-3/M82	0.97457	1
5-3/M82	0.94178	1
6-2/M82	1.0323	1
6-3/M82	0.96884	0.982
7-1/M82	0.88268	1
7-2/M82	1.03555	1
9-3-2/M82	0.87807	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.49006	0.584
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.68455	0.418
IL12-4/WTpooled	1.14598	0.839
IL1-4/WTpooled	0.91597	0.834
WT/WTpooled	1.03752	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	1.32156	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05591	0.921
DC3000/delta hrp 6h	1.84486	1
DC3000/delta hrp 12h	1.00947	1
DC3000/delta hrp 24h	1.15303	0.422

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.11052	0.063
DC3000 delta B/DC3000 delta AB	1.11335	0.381

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.1563	1
Exp 36h	1.47869	0.693
Exp 60h	1.15278	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.89728	1
Var 0h	0.83367	0.933
Var 12h I row2-row1	1.15905	0.198
Var 12h NI row2-row1	1.05234	1
Var 36h I row2-row1	0.99559	1
Var 36h NI row2-row1	1.0406	1
Var 60h I row2-row1	1.28078	0.562
Var 60h NI row2-row1	0.92327	0.977
Time course 0hI-0hNI	1.19695	0.799
Time course 12hI-12hNI	1.03716	0.754
Time course 36hI-36hNI	1.08947	0.453
Time course 60hI-60hNI	1.22787	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)	1.18022	0.289
transgenic ySAMdc/azygous control (breaker)	0.74128	0.142
transgenic ySAMdc/azygous control (red)	1.25579	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01126	0.495

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.63277	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.75041	0.172
Manapal/WT (break)	0.48083	0.333
Manapal/WT (red)	0.85922	0.607