Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.7.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.43376	0.088
27DAP/17DAP	0.77496	0.523
39DAP/27DAP	0.85306	0.495
41DAP/39DAP	0.95652	0.815
42DAP/41DAP	1.03445	0.962
43DAP/42DAP	1.2344	0.867
47DAP/43DAP	1.02078	0.966
52DAP/47DAP	1.17739	0.75
57DAP/52DAP	1.31831	0.908

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95312	0.308
17DAP/reference	0.87539	0.097
27DAP/reference	0.82408	0.03
39DAP/reference	0.77821	0.03
41DAP/reference	0.78519	0.031
42DAP/reference	0.82345	0.001
43DAP/reference	1.0125	0.942
47DAP/reference	0.84012	0.003
52DAP/reference	0.83837	0.064
57DAP/reference	0.97286	0.503

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95167	0.644
27DAP/17DAP	1.06614	0.751
39DAP/27DAP	0.85395	0.222
41DAP/39DAP	0.87741	0.347
42DAP/41DAP	1.17898	0.783
43DAP/42DAP	0.78905	0.037
47DAP/43DAP	1.00041	0.99
52DAP/47DAP	1.30604	0.517
57DAP/52DAP	1.01552	0.852
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15211	0.263
17DAP/reference	0.89336	0.295
27DAP/reference	1.06239	1
39DAP/reference	1.08981	0.601
41DAP/reference	0.89708	0.247
42DAP/reference	0.94376	0.222
43DAP/reference	1.03492	0.665
47DAP/reference	0.87665	0.128
52DAP/reference	1.11238	0.171
57DAP/reference	1.22915	0.438

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81572	0.067
17DAP/reference	0.781	0.009
27DAP/reference	1.00323	0.765
39DAP/reference	0.88707	0.159
41DAP/reference	0.88991	0.096
42DAP/reference	0.96048	0.355
43DAP/reference	0.67782	0.043
47DAP/reference	0.78312	0.017
52DAP/reference	0.71794	0.007
57DAP/reference	0.59578	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03879	0.918
17DAP/reference	1.24935	0.137
27DAP/reference	1.02053	0.903
39DAP/reference	1.24488	0.05
41DAP/reference	1.04028	0.916
42DAP/reference	1.06348	0.648
43DAP/reference	1.12821	0.572
47DAP/reference	0.81459	0.038
52DAP/reference	1.1979	0.89
57DAP/reference	1.04006	0.954

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.11921	0.966
26DAP/20DAP	0.84983	0.244
34DAP/26DAP	1.20006	0.542
51DAP/34DAP	0.85566	0.235
52DAP/51DAP	0.91977	1
53DAP/52DAP	0.78144	0.265
55DAP/53DAP	1.43316	0.041
57DAP/55DAP	0.8145	0.225
62DAP/57DAP	1.18216	0.622
68DAP/62DAP	1.26052	0.353
68DAP/14DAP	1.14902	0.311

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.66525	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.94473	0.058
Mature Green Tomato/Ripe Tomato	3.06053	0.018
Immature Eggplant/Mature Eggplant	0.99877	1
Ripe Pepper/Ripe Tomato	1.29439	1
Mature Eggplant/Ripe Tomato	1.47138

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
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	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.80523
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.71885
IL2-6/WTpooled	1.04721	1
IL7-5/WTpooled	1.44786	0.792
IL7-3/WTpooled	0.95939	1
IL12-4/WTpooled	0.87974	0.71
IL1-4/WTpooled	1.01369	1
WT/WTpooled	1.12155	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	0.83389	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92078	1
DC3000/delta hrp 6h	0.99894	0.95
DC3000/delta hrp 12h	1.4267	1
DC3000/delta hrp 24h	0.71419	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.65052	0.024
DC3000 delta B/DC3000 delta AB	0.52489	0.02

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	0.97133	1
Var 0h	1.28243	0.782
Var 12h I row2-row1	0.81811	0.467
Var 12h NI row2-row1	0.9687	0.906
Var 36h I row2-row1	0.72073	0.805
Var 36h NI row2-row1	1.32435	0.482
Var 60h I row2-row1	1.70798	0.543
Var 60h NI row2-row1	1.13554	0.904
Time course 0hI-0hNI	1.03848	0.852
Time course 12hI-12hNI	0.94015	0.368
Time course 36hI-36hNI	0.85023	0.065
Time course 60hI-60hNI	0.14445	0.005

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)	0.98441	0.789
transgenic ySAMdc/azygous control (breaker)	1.24746	0.248
transgenic ySAMdc/azygous control (red)	1.01033	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.75158	0.104

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.73434	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.6693	0.083
Manapal/WT (break)	2.62167	0.123
Manapal/WT (red)	1.53965	0.413