Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.9.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.33025	0.403
27DAP/17DAP	1.09659	0.92
39DAP/27DAP	0.92306	0.594
41DAP/39DAP	0.77924	0.233
42DAP/41DAP	1.13075	0.954
43DAP/42DAP	1.59095	0.045
47DAP/43DAP	0.87992	0.603
52DAP/47DAP	1.03336	0.946
57DAP/52DAP	0.85241	0.824

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00605	0.787
17DAP/reference	1.34003	0.08
27DAP/reference	3.27246	0.007
39DAP/reference	1.85588	0.497
41DAP/reference	1.64443	0.014
42DAP/reference	1.17437	0.027
43DAP/reference	1.21637	0.008
47DAP/reference	1.68796	0.001
52DAP/reference	0.96685	0.475
57DAP/reference	1.04974	0.447

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.47619	0.059
27DAP/17DAP	0.97325	0.887
39DAP/27DAP	0.98651	0.908
41DAP/39DAP	1.31047	0.909
42DAP/41DAP	0.92753	0.529
43DAP/42DAP	0.61062	0.022
47DAP/43DAP	0.86037	0.153
52DAP/47DAP	2.17452	0.047
57DAP/52DAP	1.08043	1
57DAP/7DAP	1.11867	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04249	0.732
17DAP/reference	1.29944	0.023
27DAP/reference	0.89717	0.082
39DAP/reference	1.26665	0.027
41DAP/reference	0.80415	0.049
42DAP/reference	0.68462	0.01
43DAP/reference	0.74994	0.032
47DAP/reference	1.07556	0.604
52DAP/reference	0.78084	0.097
57DAP/reference	0.74085	0.011

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77761	0.06
17DAP/reference	1.5458	0.008
27DAP/reference	1.17126	0.367
39DAP/reference	1.29059	0.022
41DAP/reference	0.9828	0.505
42DAP/reference	1.01112	1
43DAP/reference	1.08654	0.846
47DAP/reference	1.05412	0.712
52DAP/reference	1.06697	0.471
57DAP/reference	0.93826	0.259

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8472	0.127
17DAP/reference	0.85813	0.154
27DAP/reference	1.06219	0.552
39DAP/reference	1.21449	0.024
41DAP/reference	0.95421	0.185
42DAP/reference	0.96361	0.552
43DAP/reference	1.11428	0.459
47DAP/reference	1.54264	0.011
52DAP/reference	1.20705	0.123
57DAP/reference	1.10243	0.444

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09606	0.966
26DAP/20DAP	1.35109	1
34DAP/26DAP	0.72192	0.112
51DAP/34DAP	0.90177	0.442
52DAP/51DAP	1.10747	0.556
53DAP/52DAP	0.83287	0.076
55DAP/53DAP	1.07518	0.806
57DAP/55DAP	1.13485	0.927
62DAP/57DAP	1.04209	1
68DAP/62DAP	0.85249	0.505
68DAP/14DAP	0.49817	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.35812	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.05054	0.058
Mature Green Tomato/Ripe Tomato	1.37885	0.07
Immature Eggplant/Mature Eggplant	0.99379	1
Ripe Pepper/Ripe Tomato	0.24163	0.224
Mature Eggplant/Ripe Tomato	1.11958	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98399	0.944
1-1-2/M82	1.12615	1
12-2/M82	0.87975	0.862
12-4/M82	0.97078	1
1-3/M82	1.22321	0.479
2-1-1/M82	1.0281	1
2-1/M82	0.87554
2-6/M82	0.69818	1
3-2/M82	0.73697	0.752
4-1-1/M82	0.74049	1
4-1/M82	2.95614
4-3-2/M82	0.92565
4-3/M82	1.13786	1
5-3/M82	1.18784	1
6-2/M82	0.32286	0.481
6-3/M82	1.11429	1
7-1/M82	N/A	N/A
7-2/M82	1.97068	0.385
9-3-2/M82	0.94813	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.95119	0.473
IL7-5/WTpooled	2.00717
IL7-3/WTpooled	1.04426	1
IL12-4/WTpooled	0.94107	1
IL1-4/WTpooled	1.13307
WT/WTpooled	1.02766	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	0.92341	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02576	0.921
DC3000/delta hrp 6h	1.17919	1
DC3000/delta hrp 12h	1.37906	1
DC3000/delta hrp 24h	0.81513	0.269

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.79806	0.071
DC3000 delta B/DC3000 delta AB	0.95431	0.619

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06375	1
Exp 36h	0.70039	0.406
Exp 60h	0.73656	0.32

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01568	1
Var 0h	1.23974	0.98
Var 12h I row2-row1	0.91707	0.705
Var 12h NI row2-row1	1.1905	0.649
Var 36h I row2-row1	1.10802	1
Var 36h NI row2-row1	1.22122	0.482
Var 60h I row2-row1	0.80771	0.832
Var 60h NI row2-row1	0.95901	1
Time course 0hI-0hNI	1.25887	0.163
Time course 12hI-12hNI	0.71042	0.033
Time course 36hI-36hNI	0.56344	0.023
Time course 60hI-60hNI	0.78073	0.026

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)	1.07295	0.339
transgenic ySAMdc/azygous control (breaker)	0.60155	0.15
transgenic ySAMdc/azygous control (red)	1.02293	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.92307	0.036

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.59518	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.52925	0.172
Manapal/WT (break)	1.45575	1
Manapal/WT (red)	0.82978	0.315