Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.14.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.74178	0.123
27DAP/17DAP	1.03501	1
39DAP/27DAP	1.09525	0.919
41DAP/39DAP	1.02524	0.964
42DAP/41DAP	1.13407	0.877
43DAP/42DAP	0.80963	0.454
47DAP/43DAP	0.83775	0.496
52DAP/47DAP	0.99622	0.916
57DAP/52DAP	1.11293	0.962

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02666	0.71
17DAP/reference	1.10156	0.023
27DAP/reference	1.02021	0.82
39DAP/reference	0.98834	0.855
41DAP/reference	1.04927	0.451
42DAP/reference	0.93062	0.085
43DAP/reference	0.95625	0.448
47DAP/reference	0.89496	0.016
52DAP/reference	0.77562	0.064
57DAP/reference	0.8489	0.131

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91589	0.388
27DAP/17DAP	0.86311	0.195
39DAP/27DAP	0.83992	0.051
41DAP/39DAP	0.95544	0.861
42DAP/41DAP	1.08431	0.773
43DAP/42DAP	0.91833	0.399
47DAP/43DAP	1.04969	0.941
52DAP/47DAP	0.88792	0.603
57DAP/52DAP	0.96066	0.691
57DAP/7DAP	0.68763	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.4741	0.038
17DAP/reference	1.47212	0.006
27DAP/reference	1.53689	0.013
39DAP/reference	1.71605	0.013
41DAP/reference	1.45198	0.048
42DAP/reference	1.22056	0.024
43DAP/reference	1.85145	0.008
47DAP/reference	1.11761	0.948
52DAP/reference	1.53404	0.017
57DAP/reference	1.35511	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1027	0.164
17DAP/reference	1.07975	0.229
27DAP/reference	0.88576	0.104
39DAP/reference	0.79414	0.055
41DAP/reference	0.82378	0.016
42DAP/reference	0.82486	0.015
43DAP/reference	0.8627	0.162
47DAP/reference	0.8858	0.02
52DAP/reference	0.87876	0.007
57DAP/reference	0.99737	0.789

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.35319	0.103
17DAP/reference	1.20796	0.511
27DAP/reference	1.7574	0.018
39DAP/reference	1.56073	0.014
41DAP/reference	1.35466	0.093
42DAP/reference	1.16751	0.566
43DAP/reference	1.22401	0.599
47DAP/reference	0.86504	0.132
52DAP/reference	1.51505	0.081
57DAP/reference	0.71275	0.062

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.86805	0.585
26DAP/20DAP	1.34804	0.379
34DAP/26DAP	1.26643	0.542
51DAP/34DAP	0.79919	0.155
52DAP/51DAP	0.71451	0.151
53DAP/52DAP	1.04131	1
55DAP/53DAP	0.76271	0.065
57DAP/55DAP	1.16412	0.348
62DAP/57DAP	1.03514	1
68DAP/62DAP	0.91379	0.543
68DAP/14DAP	0.83192	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.0981	0.7

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.58066	0.058
Mature Green Tomato/Ripe Tomato	1.43469	0.018
Immature Eggplant/Mature Eggplant	0.36296	0.057
Ripe Pepper/Ripe Tomato	2.58832	0.258
Mature Eggplant/Ripe Tomato	5.70496	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.8521	0.934
1-1-2/M82	0.98634	1
12-2/M82	1.09798	1
12-4/M82	1.1502
1-3/M82	0.83657	0.441
2-1-1/M82	1.33925	0.375
2-1/M82	N/A	N/A
2-6/M82	1.15286	0.594
3-2/M82	0.85636
4-1-1/M82	1.01449	1
4-1/M82	0.996
4-3-2/M82	1.0545
4-3/M82	0.6383
5-3/M82	0.9632	1
6-2/M82	0.98161	1
6-3/M82	0.86346	0.68
7-1/M82	N/A	N/A
7-2/M82	1.04845	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	6.24558	0.277
IL2-6/WTpooled	0.94785	1
IL7-5/WTpooled	1.24492	0.635
IL7-3/WTpooled	6.27357	1
IL12-4/WTpooled	2.0498	0.516
IL1-4/WTpooled	4.43671	0.426
WT/WTpooled	0.90501	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	0.87823	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99732	1
DC3000/delta hrp 6h	1.13031	1
DC3000/delta hrp 12h	0.96567	1
DC3000/delta hrp 24h	0.90745	0.395

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.9969	1
DC3000 delta B/DC3000 delta AB	0.91084	0.23

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.92146	1
Exp 36h	0.73438	0.406
Exp 60h	0.63188	0.253

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02046	1
Var 0h	0.7349	1
Var 12h I row2-row1	0.88084	0.363
Var 12h NI row2-row1	1.09918	1
Var 36h I row2-row1	1.29581	0.908
Var 36h NI row2-row1	1.14301	1
Var 60h I row2-row1	0.91747	0.582
Var 60h NI row2-row1	0.94653	0.977
Time course 0hI-0hNI	0.92902	0.427
Time course 12hI-12hNI	0.98793	0.935
Time course 36hI-36hNI	0.9678	0.476
Time course 60hI-60hNI	0.59693	0.006

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)	0.98141	0.454
transgenic ySAMdc/azygous control (breaker)	0.89078	0.49
transgenic ySAMdc/azygous control (red)	1.12253	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98038	0.362

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.20347	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.6831	0.083
Manapal/WT (break)	1.41729	0.183
Manapal/WT (red)	1.61625	0.142