Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.11.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.37262	0.697
27DAP/17DAP	1.25572	0.849
39DAP/27DAP	1.32489	0.429
41DAP/39DAP	0.6049	0.065
42DAP/41DAP	1.20279	0.696
43DAP/42DAP	0.92905	0.874
47DAP/43DAP	1.05682	0.825
52DAP/47DAP	0.92278	0.752
57DAP/52DAP	1.49794	0.677

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87853	0.211
17DAP/reference	0.76274	0.129
27DAP/reference	0.83699	0.141
39DAP/reference	0.85442	0.261
41DAP/reference	0.8599	0.341
42DAP/reference	0.95578	0.259
43DAP/reference	1.01246	1
47DAP/reference	0.97258	0.418
52DAP/reference	1.01655	0.548
57DAP/reference	0.86966	0.044

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8691	0.336
27DAP/17DAP	1.1184	0.557
39DAP/27DAP	1.00231	1
41DAP/39DAP	1.01841	1
42DAP/41DAP	0.97812	0.776
43DAP/42DAP	1.02611	0.788
47DAP/43DAP	0.99265	0.983
52DAP/47DAP	0.95015	0.634
57DAP/52DAP	1.04217	0.978
57DAP/7DAP	0.84288	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11401	0.298
17DAP/reference	1.31491	0.016
27DAP/reference	1.08926	0.197
39DAP/reference	0.99661	0.745
41DAP/reference	1.0101	1
42DAP/reference	0.93205	0.178
43DAP/reference	1.06043	0.637
47DAP/reference	0.97911	0.671
52DAP/reference	0.96058	0.278
57DAP/reference	0.98462	0.53

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.55733	0.008
17DAP/reference	0.56088	0.005
27DAP/reference	1.11633	0.961
39DAP/reference	1.42852	0.401
41DAP/reference	1.40341	0.047
42DAP/reference	1.2551	0.108
43DAP/reference	0.7999	0.181
47DAP/reference	0.79647	0.045
52DAP/reference	0.95329	0.351
57DAP/reference	0.5276	0.013

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93248	0.268
17DAP/reference	0.93349	0.537
27DAP/reference	0.96325	0.465
39DAP/reference	1.01501	0.935
41DAP/reference	1.12438	0.065
42DAP/reference	1.52656	0.287
43DAP/reference	1.36309	0.84
47DAP/reference	1.00486	0.538
52DAP/reference	0.95743	0.573
57DAP/reference	2.60947	0.014

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.28401	0.966
26DAP/20DAP	1.68988	0.099
34DAP/26DAP	0.98652	1
51DAP/34DAP	1.03274	0.898
52DAP/51DAP	0.62673	0.151
53DAP/52DAP	0.82861	0.076
55DAP/53DAP	0.64521	0.021
57DAP/55DAP	1.11868	0.935
62DAP/57DAP	1.21938	1
68DAP/62DAP	4.77705	0.029
68DAP/14DAP	7.95143	0.065

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.22439	0.162

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.11421	0.417
Mature Green Tomato/Ripe Tomato	1.26613	0.185
Immature Eggplant/Mature Eggplant	0.93082	0.329
Ripe Pepper/Ripe Tomato	1.14268	1
Mature Eggplant/Ripe Tomato	2.0901

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.03774
12-2/M82	N/A	N/A
12-4/M82	1.28222
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
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	2.4366
4-3-2/M82	1.26619	1
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
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	1.07072	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.87425	0.243
IL2-6/WTpooled	1.17355	0.419
IL7-5/WTpooled	0.98128
IL7-3/WTpooled	1.04759	1
IL12-4/WTpooled	1.14283	0.737
IL1-4/WTpooled	1.14753	1
WT/WTpooled	1.0207	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	1.07721	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	1.03093	1
DC3000/delta hrp 12h	1.1341	1
DC3000/delta hrp 24h	0.34369

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.36882	0.076
DC3000 delta B/DC3000 delta AB	1.20126	0.209

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01105	1
Exp 36h	0.90342	0.456
Exp 60h	0.82559	0.29

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03105	1
Var 0h	0.50542	0.374
Var 12h I row2-row1	0.96345	0.948
Var 12h NI row2-row1	1.048	1
Var 36h I row2-row1	1.16238	0.41
Var 36h NI row2-row1	0.87315	0.45
Var 60h I row2-row1	0.83441	0.582
Var 60h NI row2-row1	0.86236	0.408
Time course 0hI-0hNI	0.92162	0.381
Time course 12hI-12hNI	1.05913	0.512
Time course 36hI-36hNI	1.32017	0.166
Time course 60hI-60hNI	2.09539	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)	1.00295	1
transgenic ySAMdc/azygous control (breaker)	1.22473	0.248
transgenic ySAMdc/azygous control (red)	1.09796	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.10442	0.105

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.17243	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89843	1
Manapal/WT (break)	0.96636	1
Manapal/WT (red)	0.90154	0.503