Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.1.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91124	0.456
27DAP/17DAP	0.99727	1
39DAP/27DAP	0.8477	0.304
41DAP/39DAP	1.20718	0.338
42DAP/41DAP	0.9922	1
43DAP/42DAP	1.04369	1
47DAP/43DAP	1.04216	0.842
52DAP/47DAP	1.01287	0.982
57DAP/52DAP	1.05926	0.955

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93274	0.217
17DAP/reference	0.84782	0.038
27DAP/reference	1.01956	0.934
39DAP/reference	0.84822	0.037
41DAP/reference	0.77762	0.009
42DAP/reference	1.22021	0.901
43DAP/reference	0.9091	0.36
47DAP/reference	1.00656	1
52DAP/reference	0.99973	0.689
57DAP/reference	0.95049	0.235

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92471	0.299
27DAP/17DAP	0.94509	0.648
39DAP/27DAP	1.0113	0.854
41DAP/39DAP	1.05125	0.682
42DAP/41DAP	1.11417	0.257
43DAP/42DAP	1.05245	0.162
47DAP/43DAP	1.02792	0.857
52DAP/47DAP	1.02592	0.9
57DAP/52DAP	0.99257	0.841
57DAP/7DAP	0.95251	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.39451	0.039
17DAP/reference	0.92541	0.295
27DAP/reference	1.116	0.664
39DAP/reference	0.97028	0.474
41DAP/reference	0.95945	0.431
42DAP/reference	1.10939	0.308
43DAP/reference	1.02828	0.923
47DAP/reference	1.04088	1
52DAP/reference	1.02443	0.941
57DAP/reference	0.99294	0.494

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26906	0.085
17DAP/reference	1.11774	0.69
27DAP/reference	1.12621	0.488
39DAP/reference	1.08191	0.848
41DAP/reference	1.09972	0.737
42DAP/reference	0.94289	0.261
43DAP/reference	0.89833	0.32
47DAP/reference	0.91696	0.154
52DAP/reference	1.05938	0.702
57DAP/reference	0.98577	0.68

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14194	0.493
17DAP/reference	0.97388	0.647
27DAP/reference	0.95148	0.397
39DAP/reference	1.032	0.813
41DAP/reference	1.10264	1
42DAP/reference	1.12132	0.648
43DAP/reference	1.10652	0.426
47DAP/reference	0.99654	0.646
52DAP/reference	2.14932	0.363
57DAP/reference	1.20794	0.16

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.92019	1
26DAP/20DAP	0.94302	1
34DAP/26DAP	1.03488	1
51DAP/34DAP	1.03597	0.775
52DAP/51DAP	0.9374	1
53DAP/52DAP	0.9812	0.909
55DAP/53DAP	0.97418	0.796
57DAP/55DAP	1.12835	0.826
62DAP/57DAP	1.04903	0.902
68DAP/62DAP	1.14818	0.878
68DAP/14DAP	1.48896	0.031

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.99076	0.696

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.20812	0.063
Mature Green Tomato/Ripe Tomato	0.85576	0.377
Immature Eggplant/Mature Eggplant	1.10094	0.398
Ripe Pepper/Ripe Tomato	1.41746	1
Mature Eggplant/Ripe Tomato	3.07361	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.00616	1
12-2/M82	N/A	N/A
12-4/M82	0.80385	1
1-3/M82	N/A	N/A
2-1-1/M82	0.49085
2-1/M82	N/A	N/A
2-6/M82	0.72294
3-2/M82	0.96044	1
4-1-1/M82	N/A	N/A
4-1/M82	1.32546	0.444
4-3-2/M82	0.91977
4-3/M82	0.82317
5-3/M82	1.00827
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.94801
7-2/M82	0.8824
9-3-2/M82	0.94237	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.46345
WT/WTpooled	0.80238

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	1.03997	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.24376	0.823
DC3000/delta hrp 6h	1.09479	1
DC3000/delta hrp 12h	1.08665	1
DC3000/delta hrp 24h	1.17198	0.322

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.08866	0.087
DC3000 delta B/DC3000 delta AB	1.05133	0.539

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98595	0.265
Exp 36h	1.07361	1
Exp 60h	0.98431	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02189	1
Var 0h	1.79633	0.782
Var 12h I row2-row1	1.12737	0.228
Var 12h NI row2-row1	0.94101	0.713
Var 36h I row2-row1	1.20816	0.908
Var 36h NI row2-row1	0.99597	1
Var 60h I row2-row1	1.37442	0.562
Var 60h NI row2-row1	1.05819	0.904
Time course 0hI-0hNI	1.02635	0.867
Time course 12hI-12hNI	0.97397	0.836
Time course 36hI-36hNI	0.95492	0.366
Time course 60hI-60hNI	1.16038	0.06

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)	1.01548	0.612
transgenic ySAMdc/azygous control (breaker)	0.94667	0.49
transgenic ySAMdc/azygous control (red)	0.90077	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06149	0.223

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.81732	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.78877	0.172
Manapal/WT (break)	1.36016	0.381
Manapal/WT (red)	0.89268	0.242