Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.1.12.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.35029	0.545
27DAP/17DAP	1.21018	0.895
39DAP/27DAP	3.1175	0.033
41DAP/39DAP	0.62468	0.082
42DAP/41DAP	1.50567	0.971
43DAP/42DAP	1.56587	0.861
47DAP/43DAP	1.3246	0.647
52DAP/47DAP	2.84189	0.081
57DAP/52DAP	1.27633	0.95

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90319	0.14
17DAP/reference	0.97195	0.567
27DAP/reference	1.01545	0.88
39DAP/reference	1.20684	0.074
41DAP/reference	1.15571	0.013
42DAP/reference	1.15023	0.006
43DAP/reference	1.37203	0.01
47DAP/reference	1.52389	0.001
52DAP/reference	1.06453	0.8
57DAP/reference	1.19469	0.088

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.75846	0.075
27DAP/17DAP	1.41458	0.069
39DAP/27DAP	0.97704	0.859
41DAP/39DAP	1.08589	1
42DAP/41DAP	1.43737	0.055
43DAP/42DAP	1.59322	0.017
47DAP/43DAP	1.04585	0.848
52DAP/47DAP	1.04617	0.979
57DAP/52DAP	1.69424	0.035
57DAP/7DAP	1.63442	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22877	0.144
17DAP/reference	1.18739	0.059
27DAP/reference	1.18124	0.018
39DAP/reference	1.03197	0.74
41DAP/reference	1.17663	0.077
42DAP/reference	1.30899	0.014
43DAP/reference	1.77138	0.007
47DAP/reference	1.38876	0.084
52DAP/reference	1.37606	0.013
57DAP/reference	1.18129	0.016

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94186	0.518
17DAP/reference	0.97735	0.611
27DAP/reference	0.97902	0.554
39DAP/reference	0.92731	0.33
41DAP/reference	0.95914	0.412
42DAP/reference	1.10905	0.351
43DAP/reference	0.86622	0.298
47DAP/reference	1.02969	0.916
52DAP/reference	0.8853	0.086
57DAP/reference	0.72954	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15925	0.18
17DAP/reference	0.97378	0.636
27DAP/reference	1.27259	0.045
39DAP/reference	1.37757	0.026
41DAP/reference	1.03673	0.961
42DAP/reference	1.21542	0.086
43DAP/reference	1.69503	0.007
47DAP/reference	1.48444	0.006
52DAP/reference	2.3897	0.031
57DAP/reference	2.07602	0.291

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91559	1
26DAP/20DAP	2.32028	0.131
34DAP/26DAP	0.80444	0.356
51DAP/34DAP	1.88487	0.032
52DAP/51DAP	1.26729	0.106
53DAP/52DAP	1.03765	0.845
55DAP/53DAP	0.67116	0.028
57DAP/55DAP	1.03149	0.911
62DAP/57DAP	1.3925	0.257
68DAP/62DAP	0.84468	0.29
68DAP/14DAP	1.24151	0.936

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.86493	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.46651	0.058
Mature Green Tomato/Ripe Tomato	0.27045	0.018
Immature Eggplant/Mature Eggplant	0.94122	0.448
Ripe Pepper/Ripe Tomato	0.57289	0.224
Mature Eggplant/Ripe Tomato	0.65242

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	1.49102
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	0.97757
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.70042	0.284
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.9966
7-2/M82	N/A	N/A
9-3-2/M82	1.69907

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.80521	0.473
IL7-5/WTpooled	0.9348
IL7-3/WTpooled	1.53359	1
IL12-4/WTpooled	1.05864	0.785
IL1-4/WTpooled	0.93356	1
WT/WTpooled	0.97044	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	1.0056	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	1.06366	1
DC3000/delta hrp 12h	0.8884	1
DC3000/delta hrp 24h	0.4917	0.194

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.52009	0.121
DC3000 delta B/DC3000 delta AB	1.31308	0.117

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.99276	1
Exp 36h	0.8499	0.426
Exp 60h	0.82489	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99671	1
Var 0h	0.9763	1
Var 12h I row2-row1	1.03498	1
Var 12h NI row2-row1	1.21701	0.34
Var 36h I row2-row1	0.99874	1
Var 36h NI row2-row1	0.83134	0.329
Var 60h I row2-row1	0.80358	0.285
Var 60h NI row2-row1	0.84027	0.69
Time course 0hI-0hNI	1.09338	0.662
Time course 12hI-12hNI	0.99654	1
Time course 36hI-36hNI	1.47943	0.005
Time course 60hI-60hNI	4.72395	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)	1.02516	0.748
transgenic ySAMdc/azygous control (breaker)	0.93032	0.251
transgenic ySAMdc/azygous control (red)	0.95743	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05767	0.301

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.85436	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.93661	1
Manapal/WT (break)	0.93643	1
Manapal/WT (red)	1.32004	1