Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.16.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98678	0.847
27DAP/17DAP	1.08749	0.873
39DAP/27DAP	1.06799	0.974
41DAP/39DAP	1.40084	0.359
42DAP/41DAP	0.93887	1
43DAP/42DAP	1.06221	1
47DAP/43DAP	0.86673	0.568
52DAP/47DAP	1.00543	0.976
57DAP/52DAP	1.01267	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99867	0.771
17DAP/reference	0.98358	0.664
27DAP/reference	0.97138	0.349
39DAP/reference	0.98062	0.704
41DAP/reference	1.04316	0.287
42DAP/reference	0.9559	0.05
43DAP/reference	0.94408	0.107
47DAP/reference	1.01436	0.728
52DAP/reference	1.05572	0.069
57DAP/reference	0.97749	0.395

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99228	0.826
27DAP/17DAP	0.95302	0.614
39DAP/27DAP	1.08667	0.337
41DAP/39DAP	1.0029	1
42DAP/41DAP	1.00729	1
43DAP/42DAP	1.01795	0.746
47DAP/43DAP	1.00685	0.973
52DAP/47DAP	0.98224	0.93
57DAP/52DAP	0.98156	0.75
57DAP/7DAP	0.98266	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98589	0.183
17DAP/reference	0.94352	0.013
27DAP/reference	0.96255	0.03
39DAP/reference	0.9907	0.354
41DAP/reference	1.00964	0.891
42DAP/reference	0.9888	0.482
43DAP/reference	0.94478	0.126
47DAP/reference	0.98639	0.671
52DAP/reference	0.96564	0.254
57DAP/reference	0.93103	0.026

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96674	0.58
17DAP/reference	0.96747	0.378
27DAP/reference	0.98753	0.619
39DAP/reference	1.00457	1
41DAP/reference	0.97323	0.441
42DAP/reference	0.91499	0.108
43DAP/reference	0.90197	0.108
47DAP/reference	0.87939	0.035
52DAP/reference	1.07103	0.05
57DAP/reference	0.95495	0.194

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95238	0.082
17DAP/reference	0.97282	0.508
27DAP/reference	0.97967	0.397
39DAP/reference	0.97668	0.147
41DAP/reference	0.96843	0.293
42DAP/reference	0.92531	0.059
43DAP/reference	0.98975	0.639
47DAP/reference	0.94884	0.207
52DAP/reference	0.9347	0.247
57DAP/reference	0.94679	0.288

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96832	1
26DAP/20DAP	1.03723	0.886
34DAP/26DAP	0.91232	0.272
51DAP/34DAP	1.11288	0.565
52DAP/51DAP	0.98941	1
53DAP/52DAP	0.99529	0.983
55DAP/53DAP	1.00701	1
57DAP/55DAP	1.09251	0.364
62DAP/57DAP	0.98662	0.994
68DAP/62DAP	1.00783	0.914
68DAP/14DAP	1.13502	0.189

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.98485	0.576

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.76618	0.226
Mature Green Tomato/Ripe Tomato	0.96993	0.611
Immature Eggplant/Mature Eggplant	1.19812	0.174
Ripe Pepper/Ripe Tomato	1.62712	0.233
Mature Eggplant/Ripe Tomato	0.84356	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.1167	0.877
1-1-2/M82	0.96669	1
12-2/M82	0.99257
12-4/M82	0.9476	1
1-3/M82	1.20709	0.248
2-1-1/M82	1.20091	0.366
2-1/M82	1.03455
2-6/M82	1.02212	1
3-2/M82	1.02602	0.717
4-1-1/M82	0.79347
4-1/M82	1.02136	1
4-3-2/M82	0.95502	0.698
4-3/M82	0.83592
5-3/M82	1.06037	0.572
6-2/M82	N/A	N/A
6-3/M82	0.95749
7-1/M82	0.98936
7-2/M82	1.0643	1
9-3-2/M82	1.00531	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.93374	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.34562	0.362
IL12-4/WTpooled	0.91559	0.71
IL1-4/WTpooled	1.0847	1
WT/WTpooled	0.94492	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	1.15905	0.193

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03046	0.921
DC3000/delta hrp 6h	1.03249	1
DC3000/delta hrp 12h	1.03803	1
DC3000/delta hrp 24h	1.15791	0.453

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.11932	0.121
DC3000 delta B/DC3000 delta AB	1.05304	0.477

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03568	1
Exp 36h	1.23988	0.693
Exp 60h	1.40568	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97288	1
Var 0h	1.15445	0.98
Var 12h I row2-row1	1.00892	0.795
Var 12h NI row2-row1	0.98364	0.906
Var 36h I row2-row1	0.90106	1
Var 36h NI row2-row1	0.96935	0.61
Var 60h I row2-row1	0.96077	0.582
Var 60h NI row2-row1	0.99547	1
Time course 0hI-0hNI	1.02102	0.833
Time course 12hI-12hNI	1.02856	0.663
Time course 36hI-36hNI	1.21197	0.006
Time course 60hI-60hNI	1.33245	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)	0.9992	1
transgenic ySAMdc/azygous control (breaker)	0.95034	1
transgenic ySAMdc/azygous control (red)	0.96158	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03109	0.17

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.7384	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.93007	1
Manapal/WT (break)	0.95957	1
Manapal/WT (red)	0.92315	0.607