Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.6.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93127	0.617
27DAP/17DAP	1.28467	0.783
39DAP/27DAP	0.73604	0.353
41DAP/39DAP	1.07989	0.921
42DAP/41DAP	1.08595	0.997
43DAP/42DAP	1.14157	0.778
47DAP/43DAP	0.97852	0.835
52DAP/47DAP	0.97972	0.816
57DAP/52DAP	1.15103	0.992

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10883	0.441
17DAP/reference	1.1143	0.342
27DAP/reference	1.04224	0.696
39DAP/reference	0.98304	0.75
41DAP/reference	1.05946	0.451
42DAP/reference	1.20597	0.009
43DAP/reference	1.03323	0.866
47DAP/reference	1.03093	0.708
52DAP/reference	1.1917	0.149
57DAP/reference	1.13772	0.22

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.59843	0.077
27DAP/17DAP	0.93757	0.854
39DAP/27DAP	1.21425	0.067
41DAP/39DAP	0.8828	0.804
42DAP/41DAP	1.08888	0.976
43DAP/42DAP	1.91049	0.023
47DAP/43DAP	1.06501	0.897
52DAP/47DAP	0.99008	0.925
57DAP/52DAP	1.48043	0.144
57DAP/7DAP	1.28204	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84162	0.168
17DAP/reference	0.99577	0.518
27DAP/reference	1.02136	0.8
39DAP/reference	0.99019	0.552
41DAP/reference	1.02765	0.918
42DAP/reference	1.05741	0.686
43DAP/reference	0.94364	0.321
47DAP/reference	1.2713	0.458
52DAP/reference	1.12838	1
57DAP/reference	0.96881	0.477

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9968	0.93
17DAP/reference	1.16356	0.426
27DAP/reference	1.33739	0.031
39DAP/reference	1.08064	0.556
41DAP/reference	1.15407	0.234
42DAP/reference	1.08166	0.455
43DAP/reference	1.01673	0.646
47DAP/reference	1.42142	0.019
52DAP/reference	1.00182	0.713
57DAP/reference	1.25937	0.045

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99596	0.75
17DAP/reference	0.97365	0.647
27DAP/reference	0.99582	0.843
39DAP/reference	0.77984	0.111
41DAP/reference	0.89596	0.185
42DAP/reference	1.21355	0.459
43DAP/reference	1.11623	0.474
47DAP/reference	0.85594	0.054
52DAP/reference	1.04365	0.871
57DAP/reference	1.0012	0.765

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06369	0.966
26DAP/20DAP	1.24549	0.562
34DAP/26DAP	0.92719
51DAP/34DAP	1.60265	0.207
52DAP/51DAP	0.83689	1
53DAP/52DAP	1.00913	1
55DAP/53DAP	0.71136	0.14
57DAP/55DAP	1.30875	0.915
62DAP/57DAP	0.52426	0.162
68DAP/62DAP	2.03472	0.076
68DAP/14DAP	3.93813	0.031

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.66157	0.025

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.10227	0.666
Mature Green Tomato/Ripe Tomato	1.30609	0.774
Immature Eggplant/Mature Eggplant	1.77014	0.23
Ripe Pepper/Ripe Tomato	1.56141	0.256
Mature Eggplant/Ripe Tomato	1.24541	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.3089
1-1-2/M82	1.03049	1
12-2/M82	1.02828
12-4/M82	0.84678
1-3/M82	N/A	N/A
2-1-1/M82	0.89212
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.93524	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.82115
7-2/M82	1.47258
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.89077	0.321
IL2-6/WTpooled	0.97155	1
IL7-5/WTpooled	1.07031	1
IL7-3/WTpooled	0.88618	0.294
IL12-4/WTpooled	0.89068	1
IL1-4/WTpooled	0.95998	0.699
WT/WTpooled	1.01241	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	0.80793	0.197

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.13061
DC3000/delta hrp 6h	0.95591	0.95
DC3000/delta hrp 12h	0.95921	1
DC3000/delta hrp 24h	3.22563	0.022

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.17476	1
Exp 36h	2.09055	0.489
Exp 60h	1.82359	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.11003
Var 0h	1.17275	0.98
Var 12h I row2-row1	0.97111	0.856
Var 12h NI row2-row1	1.02211	0.34
Var 36h I row2-row1	1.09859	0.41
Var 36h NI row2-row1	0.54329	1
Var 60h I row2-row1	0.87907
Var 60h NI row2-row1	0.95848	0.904
Time course 0hI-0hNI	0.95971	0.843
Time course 12hI-12hNI	1.04107	0.724
Time course 36hI-36hNI	0.86631	0.101
Time course 60hI-60hNI	0.41646	0.006

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)	1.1707	0.318
transgenic ySAMdc/azygous control (breaker)	0.92373	1
transgenic ySAMdc/azygous control (red)	1.0418	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.36107	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.50032	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	0.98453	1
Manapal/WT (red)	1.56611	0.125