Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.12.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.65933	0.142
27DAP/17DAP	0.87254	0.631
39DAP/27DAP	0.92711	0.583
41DAP/39DAP	1.19858	0.488
42DAP/41DAP	1.38077	0.856
43DAP/42DAP	0.71892	0.639
47DAP/43DAP	0.83576	0.496
52DAP/47DAP	1.30795	0.592
57DAP/52DAP	0.87016	0.803

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.55906	0.007
17DAP/reference	1.04425	0.813
27DAP/reference	0.87245	0.029
39DAP/reference	0.9568	0.575
41DAP/reference	0.98922	0.814
42DAP/reference	1.28775	0.001
43DAP/reference	0.95948	0.538
47DAP/reference	0.96626	0.258
52DAP/reference	0.88783	0.096
57DAP/reference	0.88462	0.118

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96649	0.697
27DAP/17DAP	1.03847	1
39DAP/27DAP	1.13776	0.505
41DAP/39DAP	0.98041	0.973
42DAP/41DAP	1.13509	0.708
43DAP/42DAP	0.96485	0.774
47DAP/43DAP	1.08067	0.914
52DAP/47DAP	0.97294	0.9
57DAP/52DAP	0.98979	0.784
57DAP/7DAP	1.01148	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08366	0.91
17DAP/reference	0.87487	0.02
27DAP/reference	0.81535	0.01
39DAP/reference	0.82838	0.012
41DAP/reference	0.89882	0.133
42DAP/reference	0.8224	0.011
43DAP/reference	0.80426	0.014
47DAP/reference	1.06253	0.965
52DAP/reference	0.83379	0.013
57DAP/reference	0.8733	0.114

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.37112	0.16
17DAP/reference	1.81456	0.008
27DAP/reference	1.63175	0.019
39DAP/reference	1.23111	0.424
41DAP/reference	1.65406	0.012
42DAP/reference	1.57023	0.018
43DAP/reference	1.24326	0.049
47DAP/reference	1.14395	0.059
52DAP/reference	0.96988	0.433
57DAP/reference	1.04663	0.786

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90179	0.197
17DAP/reference	1.26491	0.215
27DAP/reference	0.85425	0.047
39DAP/reference	0.93334	0.199
41DAP/reference	0.8866	0.132
42DAP/reference	1.04987	0.923
43DAP/reference	1.159	0.625
47DAP/reference	0.86136	0.066
52DAP/reference	0.75801	0.109
57DAP/reference	1.11364	0.682

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94766	1
26DAP/20DAP	0.95482	1
34DAP/26DAP	1.03399	1
51DAP/34DAP	0.9145	0.442
52DAP/51DAP	0.9924	1
53DAP/52DAP	1.0271	0.944
55DAP/53DAP	1.17857	0.487
57DAP/55DAP	0.99312	0.845
62DAP/57DAP	1.25924	0.622
68DAP/62DAP	0.75699	0.429
68DAP/14DAP	0.69361	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.92654	0.399

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.59731	0.113
Mature Green Tomato/Ripe Tomato	0.99107	0.774
Immature Eggplant/Mature Eggplant	1.23731	0.267
Ripe Pepper/Ripe Tomato	0.62727
Mature Eggplant/Ripe Tomato	2.15474	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05803	1
1-1-2/M82	0.95271
12-2/M82	1.06586
12-4/M82	1.04796
1-3/M82	1.07437	1
2-1-1/M82	0.92916
2-1/M82	N/A	N/A
2-6/M82	0.9571	1
3-2/M82	0.85733
4-1-1/M82	0.93816	1
4-1/M82	0.95532
4-3-2/M82	0.97831
4-3/M82	0.93825	0.72
5-3/M82	0.98648	1
6-2/M82	0.92688	1
6-3/M82	1.62914
7-1/M82	N/A	N/A
7-2/M82	0.95304	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.15387
IL2-6/WTpooled	1.14781	0.531
IL7-5/WTpooled	1.35777	0.792
IL7-3/WTpooled	1.01913	1
IL12-4/WTpooled	0.94801	1
IL1-4/WTpooled	1.24157	1
WT/WTpooled	0.97559	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	1.00422	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99386	1
DC3000/delta hrp 6h	1.1399	1
DC3000/delta hrp 12h	1.01915	1
DC3000/delta hrp 24h	1.00363	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.64516	0.029
DC3000 delta B/DC3000 delta AB	0.48925	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.21668	1
Exp 36h	1.03255	1
Exp 60h	0.72343	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00124	1
Var 0h	1.35844	0.98
Var 12h I row2-row1	0.97632	0.948
Var 12h NI row2-row1	1.1726	1
Var 36h I row2-row1	0.71622	0.805
Var 36h NI row2-row1	0.92045	0.706
Var 60h I row2-row1	1.08376	1
Var 60h NI row2-row1	1.05946	0.904
Time course 0hI-0hNI	1.01902	0.867
Time course 12hI-12hNI	0.88221	0.47
Time course 36hI-36hNI	0.85136	0.025
Time course 60hI-60hNI	0.43147	0.007

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)	1.12915	0.372
transgenic ySAMdc/azygous control (breaker)	0.97768	1
transgenic ySAMdc/azygous control (red)	1.1368	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0379	0.421

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.19755	0.228

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	41.9995	0.083
Manapal/WT (break)	1.13328	1
Manapal/WT (red)	0.70164	0.274