Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.11.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02594	0.932
27DAP/17DAP	1.09362	0.859
39DAP/27DAP	0.95135	0.62
41DAP/39DAP	1.00466	0.909
42DAP/41DAP	0.9876	1
43DAP/42DAP	0.97165	0.91
47DAP/43DAP	1.08848	0.756
52DAP/47DAP	0.83019	0.545
57DAP/52DAP	1.05912	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00024	1
17DAP/reference	0.9742	0.503
27DAP/reference	1.03093	0.539
39DAP/reference	1.0091	0.786
41DAP/reference	1.04253	0.019
42DAP/reference	1.05635	0.025
43DAP/reference	1.02029	0.758
47DAP/reference	1.0362	0.142
52DAP/reference	1.01482	0.73
57DAP/reference	1.01646	0.845

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99907	1
27DAP/17DAP	1.05045	0.9
39DAP/27DAP	0.99632	1
41DAP/39DAP	1.02048	0.849
42DAP/41DAP	0.98152	0.777
43DAP/42DAP	1.03294	0.273
47DAP/43DAP	0.99159	0.947
52DAP/47DAP	1.03702	0.844
57DAP/52DAP	1.0099	0.992
57DAP/7DAP	1.0367	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86806	0.146
17DAP/reference	0.89449	0.011
27DAP/reference	0.85289	0.01
39DAP/reference	0.85951	0.014
41DAP/reference	0.88443	0.023
42DAP/reference	0.83091	0.012
43DAP/reference	0.82957	0.024
47DAP/reference	0.88238	0.04
52DAP/reference	0.88905	0.061
57DAP/reference	0.87873	0.039

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95524	0.362
17DAP/reference	1.00361	0.873
27DAP/reference	0.92323	0.076
39DAP/reference	0.9456	0.126
41DAP/reference	0.99235	0.584
42DAP/reference	1.01501	1
43DAP/reference	1.07315	0.205
47DAP/reference	1.02636	0.353
52DAP/reference	0.96079	0.22
57DAP/reference	1.01178	0.786

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89336	0.071
17DAP/reference	0.9703	0.508
27DAP/reference	0.88745	0.038
39DAP/reference	0.95177	0.299
41DAP/reference	0.8828	0.025
42DAP/reference	0.77055	0.016
43DAP/reference	0.87627	0.018
47DAP/reference	0.98381	0.593
52DAP/reference	0.91075	0.351
57DAP/reference	1.06274	0.385

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96956	0.672
26DAP/20DAP	1.02074	1
34DAP/26DAP	1.02641	0.819
51DAP/34DAP	0.97104	0.743
52DAP/51DAP	0.9586	1
53DAP/52DAP	1.12404	0.47
55DAP/53DAP	1.04789	0.748
57DAP/55DAP	0.81194	0.264
62DAP/57DAP	1.04684	0.833
68DAP/62DAP	0.97795	0.834
68DAP/14DAP	1.06533	0.762

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.01371	0.865

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.00971	0.886
Mature Green Tomato/Ripe Tomato	0.85523	0.148
Immature Eggplant/Mature Eggplant	1.27927	0.311
Ripe Pepper/Ripe Tomato	1.38012	1
Mature Eggplant/Ripe Tomato	1.51236	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98068	0.961
1-1-2/M82	0.92417	0.804
12-2/M82	0.96316	0.955
12-4/M82	0.99586	1
1-3/M82	0.94156	0.441
2-1-1/M82	0.83984	0.565
2-1/M82	1.07758	1
2-6/M82	0.95961	0.501
3-2/M82	1.02576	1
4-1-1/M82	1.02144	1
4-1/M82	0.59124	1
4-3-2/M82	0.7408	0.487
4-3/M82	0.8886	1
5-3/M82	0.95736	1
6-2/M82	1.01273	1
6-3/M82	1.06978	1
7-1/M82	0.95056	1
7-2/M82	0.90703	0.881
9-3-2/M82	0.79158	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.16236
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.00483
IL12-4/WTpooled	0.98739	1
IL1-4/WTpooled	1.03804	1
WT/WTpooled	0.98701	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	1.19222

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01565	0.921
DC3000/delta hrp 6h	1.53179	1
DC3000/delta hrp 12h	1.00283	1
DC3000/delta hrp 24h	1.00633	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.09518	0.121
DC3000 delta B/DC3000 delta AB	1.11092	0.311

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00062	1
Var 0h	0.43941	0.202
Var 12h I row2-row1	1.12423	0.196
Var 12h NI row2-row1	1.04941	0.649
Var 36h I row2-row1	1.03244	1
Var 36h NI row2-row1	0.90877	0.645
Var 60h I row2-row1	1.09767	0.562
Var 60h NI row2-row1	1.10427	1
Time course 0hI-0hNI	1.08357	0.852
Time course 12hI-12hNI	0.9963	1
Time course 36hI-36hNI	0.9477	0.156
Time course 60hI-60hNI	1.16261	0.029

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)	0.98264	0.789
transgenic ySAMdc/azygous control (breaker)	1.22066	1
transgenic ySAMdc/azygous control (red)	1.47203	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97146	0.242

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.0763	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.31894	0.307
Manapal/WT (break)	1.35273	1
Manapal/WT (red)	0.71312	0.216