Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.3.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92097	0.486
27DAP/17DAP	1.42489	0.617
39DAP/27DAP	1.15973	0.759
41DAP/39DAP	1.47394	0.708
42DAP/41DAP	0.79167	0.774
43DAP/42DAP	3.34549	0.072
47DAP/43DAP	0.43637	0.049
52DAP/47DAP	1.52339	0.424
57DAP/52DAP	0.87793	0.89

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13385	0.078
17DAP/reference	0.971	0.63
27DAP/reference	0.97634	0.61
39DAP/reference	0.9786	0.797
41DAP/reference	1.01573	1
42DAP/reference	1.62268	0.001
43DAP/reference	1.21547
47DAP/reference	1.21434	0.558
52DAP/reference	1.28877	0.03
57DAP/reference	0.72546

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89063	0.484
27DAP/17DAP	1.39905	0.069
39DAP/27DAP	0.86049	0.269
41DAP/39DAP	0.9774	0.98
42DAP/41DAP	0.90411	0.315
43DAP/42DAP	0.92381	0.431
47DAP/43DAP	1.17939	0.817
52DAP/47DAP	1.56693	0.082
57DAP/52DAP	1.07709	0.686
57DAP/7DAP	1.09338	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.64279	0.091
17DAP/reference	0.60817	0.012
27DAP/reference	0.72556	0.01
39DAP/reference	0.70643	0.031
41DAP/reference	0.63577	0.025
42DAP/reference	0.88594	0.235
43DAP/reference	0.91815	0.202
47DAP/reference	1.20742	0.195
52DAP/reference	0.62168	0.014
57DAP/reference	0.88333	0.156

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96831	0.669
17DAP/reference	1.09753	0.437
27DAP/reference	1.19619	0.056
39DAP/reference	1.21094	0.449
41DAP/reference	1.31254	0.48
42DAP/reference	1.15449	0.294
43DAP/reference	1.17638	0.429
47DAP/reference	1.11345	0.143
52DAP/reference	1.09201	0.181
57DAP/reference	0.98265	0.649

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.59898	0.055
17DAP/reference	0.9735	0.615
27DAP/reference	0.70017	0.038
39DAP/reference	0.64586	0.018
41DAP/reference	0.62474	0.058
42DAP/reference	0.79954	0.172
43DAP/reference	1.13944	0.712
47DAP/reference	1.18224	0.324
52DAP/reference	1.05958	0.77
57DAP/reference	2.48641	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16862	0.966
26DAP/20DAP	2.00623	0.249
34DAP/26DAP	0.74931	0.419
51DAP/34DAP	1.49193	0.293
52DAP/51DAP	1.45982	0.035
53DAP/52DAP	1.0829	0.944
55DAP/53DAP	0.99724	0.908
57DAP/55DAP	1.25767	0.559
62DAP/57DAP	1.87583	0.002
68DAP/62DAP	1.19145	0.831
68DAP/14DAP	2.13881	0.029

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.31101	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.82147	0.276
Mature Green Tomato/Ripe Tomato	0.89841	0.611
Immature Eggplant/Mature Eggplant	0.99625	1
Ripe Pepper/Ripe Tomato	0.85235	0.224
Mature Eggplant/Ripe Tomato	1.1356	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.13837	1
1-3/M82	N/A	N/A
2-1-1/M82	0.83029
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	0.80653
4-3/M82	N/A	N/A
5-3/M82	1.16553	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.97953

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.97777	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.27759	1
IL7-3/WTpooled	1.09122
IL12-4/WTpooled	1.14197	0.891
IL1-4/WTpooled	1.05984	1
WT/WTpooled	0.90134	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	0.93441	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96029	1
DC3000/delta hrp 6h	1.01895	0.95
DC3000/delta hrp 12h	1.03184	1
DC3000/delta hrp 24h	1.98564	0.03

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.76429
DC3000 delta B/DC3000 delta AB	0.98757	0.961

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94091	1
Exp 36h	1.33503	0.693
Exp 60h	1.28194	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.38376	0.325
Var 12h I row2-row1	0.76129	0.565
Var 12h NI row2-row1	2.80558	0.281
Var 36h I row2-row1	1.03998	1
Var 36h NI row2-row1	0.48886	0.478
Var 60h I row2-row1	0.89289	0.832
Var 60h NI row2-row1	0.74177	0.458
Time course 0hI-0hNI	1.61159
Time course 12hI-12hNI	2.39571
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)	1.01477	0.798
transgenic ySAMdc/azygous control (breaker)	1.10017	1
transgenic ySAMdc/azygous control (red)	1.02243	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03309	0.083

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.96668	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.02042	0.105
Manapal/WT (break)	0.70268	1
Manapal/WT (red)	1.15311	1