Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.4.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.39348	0.183
27DAP/17DAP	1.25996	0.785
39DAP/27DAP	1.00612	1
41DAP/39DAP	1.01577	1
42DAP/41DAP	1.093	0.912
43DAP/42DAP	1.26615	0.861
47DAP/43DAP	1.07486	0.95
52DAP/47DAP	1.16213	0.96
57DAP/52DAP	0.88635	0.853

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81792	0.041
17DAP/reference	0.85164	0.097
27DAP/reference	1.08979	0.394
39DAP/reference	1.0029	1
41DAP/reference	0.83777	0.031
42DAP/reference	0.81494	0.007
43DAP/reference	1.04603	0.403
47DAP/reference	1.03723	0.627
52DAP/reference	1.30562	0.01
57DAP/reference	1.26556	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1192	0.515
27DAP/17DAP	1.05443	0.9
39DAP/27DAP	0.88466	0.432
41DAP/39DAP	1.1293	0.674
42DAP/41DAP	0.93661	0.524
43DAP/42DAP	0.87351	0.127
47DAP/43DAP	1.07532	0.848
52DAP/47DAP	1.24031	0.504
57DAP/52DAP	0.9825	0.813
57DAP/7DAP	1.00356	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89411	0.183
17DAP/reference	0.88864	0.167
27DAP/reference	0.90175	0.146
39DAP/reference	0.92885	0.198
41DAP/reference	0.85611	0.05
42DAP/reference	0.84972	0.025
43DAP/reference	0.77221	0.033
47DAP/reference	0.98626	0.671
52DAP/reference	0.76283	0.016
57DAP/reference	0.93655	0.27

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87919	0.475
17DAP/reference	0.87184	0.176
27DAP/reference	0.88853	0.062
39DAP/reference	1.06258	0.956
41DAP/reference	1.02162	1
42DAP/reference	0.895	0.061
43DAP/reference	0.797	0.144
47DAP/reference	0.97212	0.379
52DAP/reference	1.01926	0.713
57DAP/reference	0.84953	0.384

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91343	0.362
17DAP/reference	0.98195	0.647
27DAP/reference	0.8474	0.065
39DAP/reference	0.80295	0.033
41DAP/reference	0.88218	0.148
42DAP/reference	0.80385	0.134
43DAP/reference	0.91979	0.281
47DAP/reference	0.96256	0.409
52DAP/reference	0.97719	0.747
57DAP/reference	1.03855	0.604

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99864	1
26DAP/20DAP	0.91822	0.512
34DAP/26DAP	1.20268	1
51DAP/34DAP	1.16458	0.785
52DAP/51DAP	1.03501	0.965
53DAP/52DAP	1.28623	0.845
55DAP/53DAP	0.99866	0.917
57DAP/55DAP	1.02066	0.867
62DAP/57DAP	0.84376	0.681
68DAP/62DAP	1.13231	0.897
68DAP/14DAP	2.01683	0.045

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.67176	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.29671	0.086
Mature Green Tomato/Ripe Tomato	0.90062	0.522
Immature Eggplant/Mature Eggplant	1.15198	0.58
Ripe Pepper/Ripe Tomato	0.50548	0.224
Mature Eggplant/Ripe Tomato	0.45996	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.93421
1-1-2/M82	1.19982	0.977
12-2/M82	0.66629	0.535
12-4/M82	1.20137	1
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	N/A	N/A
4-3-2/M82	1.38388
4-3/M82	N/A	N/A
5-3/M82	1.05779	1
6-2/M82	0.74548
6-3/M82	0.91167	1
7-1/M82	N/A	N/A
7-2/M82	0.95419
9-3-2/M82	1.15477	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.11048	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.27387	1
IL12-4/WTpooled	1.13492	0.839
IL1-4/WTpooled	0.86329
WT/WTpooled	1.1744	0.785

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	1.01882	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06416	0.921
DC3000/delta hrp 6h	1.00067	0.95
DC3000/delta hrp 12h	1.04085	1
DC3000/delta hrp 24h	1.20575	0.271

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.54693	0.042
DC3000 delta B/DC3000 delta AB	1.67231

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07366	1
Exp 36h	1.21779	1
Exp 60h	1.06457	1

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.91758	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.13625	0.408
transgenic ySAMdc/azygous control (breaker)	1.297	0.248
transgenic ySAMdc/azygous control (red)	0.88232	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.14088	0.061

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.71957	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.66036	0.172
Manapal/WT (break)	0.69579	0.299
Manapal/WT (red)	1.09457	0.413