Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.4.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.81607	0.303
27DAP/17DAP	2.73381	0.087
39DAP/27DAP	2.35109	0.028
41DAP/39DAP	0.95403	0.73
42DAP/41DAP	0.7338	0.774
43DAP/42DAP	1.07748	1
47DAP/43DAP	0.70524	0.165
52DAP/47DAP	0.78728	0.488
57DAP/52DAP	1.12983	0.952

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.73716	0.028
17DAP/reference	0.79091	0.009
27DAP/reference	0.83744	0.083
39DAP/reference	1.20452	0.191
41DAP/reference	0.98959	0.814
42DAP/reference	1.68581	0.005
43DAP/reference	1.35469	0.009
47DAP/reference	1.29122	0.575
52DAP/reference	0.86372	0.089
57DAP/reference	1.05523	0.496

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.43964	0.066
27DAP/17DAP	2.04925	0.035
39DAP/27DAP	1.75009	0.124
41DAP/39DAP	0.45048	0.016
42DAP/41DAP	1.93004	0.015
43DAP/42DAP	2.55966	0.018
47DAP/43DAP	0.66125	0.015
52DAP/47DAP	2.04505	0.082
57DAP/52DAP	1.14052	1
57DAP/7DAP	2.8112	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77708	0.08
17DAP/reference	0.7339	0.064
27DAP/reference	1.12455	0.16
39DAP/reference	1.28889	0.015
41DAP/reference	1.22041	0.314
42DAP/reference	1.55423	0.018
43DAP/reference	1.08327	0.873
47DAP/reference	1.66419	0.049
52DAP/reference	0.65117	0.02
57DAP/reference	0.74048	0.018

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78795	0.17
17DAP/reference	0.77232	0.063
27DAP/reference	1.58393	0.182
39DAP/reference	1.07898	1
41DAP/reference	1.49844	0.008
42DAP/reference	1.26314	0.17
43DAP/reference	1.62491	0.061
47DAP/reference	1.40874	0.02
52DAP/reference	0.82182	0.055
57DAP/reference	0.8997	0.338

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77601	0.057
17DAP/reference	0.82247	0.159
27DAP/reference	0.99229	0.763
39DAP/reference	1.16647	0.318
41DAP/reference	1.59585	0.025
42DAP/reference	1.51664	0.124
43DAP/reference	1.77936	0.044
47DAP/reference	1.99018	0.005
52DAP/reference	1.75761	0.132
57DAP/reference	1.30928	0.031

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02324	0.966
26DAP/20DAP	1.29045	0.608
34DAP/26DAP	1.98149	1
51DAP/34DAP	1.16198	0.677
52DAP/51DAP	1.18486	0.836
53DAP/52DAP	0.75013	0.371
55DAP/53DAP	0.81558	0.544
57DAP/55DAP	0.75386
62DAP/57DAP	0.86272	0.871
68DAP/62DAP	1.06151
68DAP/14DAP	1.13703	0.558

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	12.5837	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	3.9027	0.015
Immature Eggplant/Mature Eggplant	1.33539	0.058
Ripe Pepper/Ripe Tomato	0.09158	0.224
Mature Eggplant/Ripe Tomato	4.01903	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.72271	0.477
1-1-2/M82	1.17992	1
12-2/M82	N/A	N/A
12-4/M82	1.36771
1-3/M82	1.74163
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.5909	1
3-2/M82	4.10073
4-1-1/M82	0.74985
4-1/M82	1.18625
4-3-2/M82	0.5649	0.487
4-3/M82	0.98653	1
5-3/M82	1.07836	1
6-2/M82	1.72786	0.188
6-3/M82	1.28192	1
7-1/M82	1.66153
7-2/M82	0.90729	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.78611	0.321
IL2-6/WTpooled	1.15744	0.584
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.03862	0.362
IL12-4/WTpooled	1.06294	0.737
IL1-4/WTpooled	0.88652	0.699
WT/WTpooled	1.03213	0.85

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	1.4675	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.27079	0.846
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.05412	1
DC3000/delta hrp 24h	2.53918	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.83816	0.042
DC3000 delta B/DC3000 delta AB	1.38496	0.122

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.21825	1
Exp 36h	3.64544	0.693
Exp 60h	1.87541	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.07359
Var 0h	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.51777	0.255
transgenic ySAMdc/azygous control (breaker)	0.95632	1
transgenic ySAMdc/azygous control (red)	0.91238	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.09554	0.066

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.70309	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.45559	0.172
Manapal/WT (break)	0.68297	1
Manapal/WT (red)	0.67748	0.274