Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.20.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01373	0.847
27DAP/17DAP	0.68935	0.124
39DAP/27DAP	1.33457	0.903
41DAP/39DAP	1.0251	0.939
42DAP/41DAP	1.0158	1
43DAP/42DAP	1.0988	1
47DAP/43DAP	1.94529	0.52
52DAP/47DAP	1.0335	0.81
57DAP/52DAP	0.89091	0.923

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89321	0.162
17DAP/reference	1.05804	0.185
27DAP/reference	0.98447	0.711
39DAP/reference	0.97499	0.651
41DAP/reference	0.87989	0.434
42DAP/reference	0.8848	0.005
43DAP/reference	0.93551	0.234
47DAP/reference	0.93532	0.077
52DAP/reference	0.73469	0.042
57DAP/reference	0.87895	0.091

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88725	0.509
27DAP/17DAP	1.04732	0.923
39DAP/27DAP	0.89134	0.556
41DAP/39DAP	0.99389	1
42DAP/41DAP	0.99478	0.845
43DAP/42DAP	0.96505	0.729
47DAP/43DAP	1.02511	0.956
52DAP/47DAP	0.96799	0.893
57DAP/52DAP	0.94827	0.668
57DAP/7DAP	1.03239	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29565	0.126
17DAP/reference	1.26088	0.437
27DAP/reference	1.06531	0.664
39DAP/reference	0.9525	0.198
41DAP/reference	1.05349	0.655
42DAP/reference	0.94168	0.338
43DAP/reference	1.1083	0.2
47DAP/reference	1.03679	0.776
52DAP/reference	1.19242	0.025
57DAP/reference	1.15999	0.232

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88031	0.096
17DAP/reference	0.85307	0.047
27DAP/reference	0.86201	0.129
39DAP/reference	0.85742	0.013
41DAP/reference	0.92676	0.115
42DAP/reference	0.81283	0.016
43DAP/reference	0.83585	0.082
47DAP/reference	0.80488	0.025
52DAP/reference	0.89003	0.005
57DAP/reference	0.75269	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13063	0.13
17DAP/reference	0.96169	0.601
27DAP/reference	0.96384	0.465
39DAP/reference	1.18615	0.245
41DAP/reference	1.18746	0.333
42DAP/reference	1.2513	0.189
43DAP/reference	1.37673	0.355
47DAP/reference	1.02344	0.877
52DAP/reference	1.07418	0.714
57DAP/reference	1.24713	0.09

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09013	0.817
26DAP/20DAP	0.97583	1
34DAP/26DAP	0.99102	0.988
51DAP/34DAP	1.10955	0.785
52DAP/51DAP	1.16757	0.171
53DAP/52DAP	1.23271	0.413
55DAP/53DAP	0.97089	0.807
57DAP/55DAP	1.05223	1
62DAP/57DAP	1.3591	0.767
68DAP/62DAP	1.11765	0.939
68DAP/14DAP	1.21491	0.521

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02013	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.94476	0.591
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.28399	0.165
Ripe Pepper/Ripe Tomato	0.64171	0.293
Mature Eggplant/Ripe Tomato	0.77864	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02082	1
1-1-2/M82	0.80852	1
12-2/M82	1.09537	1
12-4/M82	0.93986	1
1-3/M82	0.90544	0.501
2-1-1/M82	1.21242	0.439
2-1/M82	1.00522	1
2-6/M82	1.30237	0.452
3-2/M82	0.92737
4-1-1/M82	N/A	N/A
4-1/M82	0.97712
4-3-2/M82	0.99326
4-3/M82	0.98556	1
5-3/M82	1.11047	0.496
6-2/M82	1.10369	1
6-3/M82	0.99729	1
7-1/M82	N/A	N/A
7-2/M82	1.10693	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.07603	1
IL2-6/WTpooled	0.7334	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.05739	1
IL12-4/WTpooled	1.16638	0.503
IL1-4/WTpooled	0.97608	1
WT/WTpooled	0.99338	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	1.24152	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95256	1
DC3000/delta hrp 6h	0.92546	0.95
DC3000/delta hrp 12h	0.92294	1
DC3000/delta hrp 24h	1.05348	0.483

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.92432
DC3000 delta B/DC3000 delta AB	1.17853	0.381

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.84094	1
Exp 36h	1.28718	1
Exp 60h	1.29002	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.93181	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.10959	0.795
Var 12h NI row2-row1	0.82023	0.82
Var 36h I row2-row1	0.90622	0.805
Var 36h NI row2-row1	0.93842	0.743
Var 60h I row2-row1	0.77237	0.306
Var 60h NI row2-row1	1.1838	0.904
Time course 0hI-0hNI	0.98031	0.927
Time course 12hI-12hNI	1.00045	1
Time course 36hI-36hNI	1.10368	0.651
Time course 60hI-60hNI	1.80688	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)	1.09288	0.318
transgenic ySAMdc/azygous control (breaker)	1.23101	1
transgenic ySAMdc/azygous control (red)	1.12138	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00368	0.811

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.27782	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89722	1
Manapal/WT (break)	0.93421	1
Manapal/WT (red)	0.83982	0.36