Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.4.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06064	0.77
27DAP/17DAP	1.19282	0.854
39DAP/27DAP	0.84157	0.435
41DAP/39DAP	1.42842	0.413
42DAP/41DAP	0.95291	1
43DAP/42DAP	0.98754	0.931
47DAP/43DAP	1.01122	0.979
52DAP/47DAP	1.25158	0.731
57DAP/52DAP	0.95356	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99778	0.771
17DAP/reference	1.00556	0.787
27DAP/reference	0.87173	0.359
39DAP/reference	0.91125
41DAP/reference	0.99038	1
42DAP/reference	1.2729	0.231
43DAP/reference	0.88845
47DAP/reference	1.03104	0.495
52DAP/reference	1.0104	1
57DAP/reference	0.34315

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02911	0.762
27DAP/17DAP	1.09687	0.686
39DAP/27DAP	0.97598	0.732
41DAP/39DAP	0.97499	0.959
42DAP/41DAP	1.01823	0.872
43DAP/42DAP	1.004	0.788
47DAP/43DAP	1.00351	0.973
52DAP/47DAP	0.97425	0.9
57DAP/52DAP	1.00187	1
57DAP/7DAP	0.96355	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03411	0.718
17DAP/reference	1.14866	0.01
27DAP/reference	1.20865	0.009
39DAP/reference	1.12705	0.023
41DAP/reference	1.09752	0.077
42DAP/reference	1.22559	0.009
43DAP/reference	1.24149	0.019
47DAP/reference	1.11089	0.604
52DAP/reference	1.20968	0.029
57DAP/reference	1.18688	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98994	0.869
17DAP/reference	0.84732	0.047
27DAP/reference	1.00767	1
39DAP/reference	0.975	0.077
41DAP/reference	0.97566	0.441
42DAP/reference	0.94327	0.098
43DAP/reference	0.95379	0.468
47DAP/reference	0.94763	0.107
52DAP/reference	0.88584	0.093
57DAP/reference	0.97146	0.581

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08075	0.251
17DAP/reference	1.0015	1
27DAP/reference	1.1057	0.156
39DAP/reference	1.0271	0.733
41DAP/reference	1.0892	0.15
42DAP/reference	1.09693	0.272
43DAP/reference	1.05751	0.59
47DAP/reference	0.90266	0.048
52DAP/reference	1.18275	0.241
57DAP/reference	0.99921	0.73

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02056	0.966
26DAP/20DAP	0.95172	0.512
34DAP/26DAP	1.05856	0.819
51DAP/34DAP	1.09756	0.365
52DAP/51DAP	1.02998	0.783
53DAP/52DAP	1.0279	0.91
55DAP/53DAP	1.03426	0.842
57DAP/55DAP	0.98198	0.902
62DAP/57DAP	0.66569
68DAP/62DAP	1.18761	0.353
68DAP/14DAP	1.41907	0.035

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.0676	0.212

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.71473	0.234
Mature Green Tomato/Ripe Tomato	0.72533	0.132
Immature Eggplant/Mature Eggplant	0.9694	0.912
Ripe Pepper/Ripe Tomato	2.38702	1
Mature Eggplant/Ripe Tomato	1.59204	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.91239	0.944
1-1-2/M82	0.95476	0.958
12-2/M82	0.99173	1
12-4/M82	0.99933	1
1-3/M82	1.01515	1
2-1-1/M82	0.97699	1
2-1/M82	0.83035	0.325
2-6/M82	0.944	1
3-2/M82	1.01602	1
4-1-1/M82	1.02802	1
4-1/M82	0.93044	1
4-3-2/M82	0.86482	0.487
4-3/M82	0.93102	0.72
5-3/M82	1.03358	1
6-2/M82	1.13419	1
6-3/M82	1.06725	1
7-1/M82	1.07827	0.992
7-2/M82	0.84571	0.796
9-3-2/M82	0.93479	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.36547	0.277
IL2-6/WTpooled	0.78117	0.473
IL7-5/WTpooled	0.86982	1
IL7-3/WTpooled	1.27924	1
IL12-4/WTpooled	1.22062	0.839
IL1-4/WTpooled	0.77006	0.415
WT/WTpooled	1.07938	0.789

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	0.83181	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0335	0.846
DC3000/delta hrp 6h	1.08034	0.95
DC3000/delta hrp 12h	0.95529	1
DC3000/delta hrp 24h	1.0633	0.582

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.19311	0.121
DC3000 delta B/DC3000 delta AB	1.29712	0.217

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.16696	1
Exp 36h	2.43988	0.693
Exp 60h	1.16247	1

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	1.2392	0.263
Var 12h I row2-row1	0.76555
Var 12h NI row2-row1	1.18292	1
Var 36h I row2-row1	1.26078	0.283
Var 36h NI row2-row1	0.89541	0.706
Var 60h I row2-row1	0.6798
Var 60h NI row2-row1	0.94862	0.932
Time course 0hI-0hNI	1.03657	1
Time course 12hI-12hNI	0.8847	0.575
Time course 36hI-36hNI	1.20747	0.248
Time course 60hI-60hNI	1.30549	0.302

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)	0.90636	0.377
transgenic ySAMdc/azygous control (breaker)	1.28162	1
transgenic ySAMdc/azygous control (red)	1.31471	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02346	0.372

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.35971	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.79027	1
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.77191	0.181