Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.18.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.26662	0.725
27DAP/17DAP	1.38163	0.677
39DAP/27DAP	1.7478	0.53
41DAP/39DAP	1.08959	0.797
42DAP/41DAP	0.88978	1
43DAP/42DAP	1.55239	0.52
47DAP/43DAP	1.06549	0.701
52DAP/47DAP	1.14779	0.969
57DAP/52DAP	1.2183	0.992

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79226	0.024
17DAP/reference	1.04229	0.585
27DAP/reference	0.94141	0.395
39DAP/reference	1.12406	0.086
41DAP/reference	1.30436	0.014
42DAP/reference	1.22588	0.029
43DAP/reference	1.52195	0.009
47DAP/reference	1.71995	0.03
52DAP/reference	1.1179	0.453
57DAP/reference	0.9927	0.671

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86406	0.428
27DAP/17DAP	1.1164	0.881
39DAP/27DAP	1.12448	0.512
41DAP/39DAP	1.03174	0.896
42DAP/41DAP	0.865	0.206
43DAP/42DAP	1.26628	0.212
47DAP/43DAP	1.04005	0.93
52DAP/47DAP	1.02719	0.927
57DAP/52DAP	0.98726	0.798
57DAP/7DAP	1.03131	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00301	1
17DAP/reference	0.99691	0.599
27DAP/reference	0.95803	0.402
39DAP/reference	1.04459	0.819
41DAP/reference	1.02442	0.848
42DAP/reference	0.93304	0.32
43DAP/reference	1.12721	0.273
47DAP/reference	1.11289	0.537
52DAP/reference	1.12839	0.328
57DAP/reference	1.26928	0.031

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91841	0.386
17DAP/reference	1.00426	0.851
27DAP/reference	1.06338	1
39DAP/reference	0.9318	0.298
41DAP/reference	0.85394	0.083
42DAP/reference	1.00007	1
43DAP/reference	1.35484	0.076
47DAP/reference	1.06677	0.658
52DAP/reference	0.95593	0.259
57DAP/reference	1.06389	0.552

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89183	0.23
17DAP/reference	1.03916	0.988
27DAP/reference	1.00402	0.727
39DAP/reference	1.05996	0.528
41DAP/reference	0.99264	0.682
42DAP/reference	0.98564	0.671
43DAP/reference	1.25657	0.465
47DAP/reference	1.81883	0.005
52DAP/reference	1.32567	0.262
57DAP/reference	0.92828	0.268

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98203	1
26DAP/20DAP	0.7633	0.244
34DAP/26DAP	1.21253	1
51DAP/34DAP	0.95016	0.703
52DAP/51DAP	1.02636	0.888
53DAP/52DAP	1.18006	0.47
55DAP/53DAP	1.03271	0.982
57DAP/55DAP	0.83405	0.403
62DAP/57DAP	0.77583	0.088
68DAP/62DAP	0.8241	0.406
68DAP/14DAP	0.66736	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.83507	0.108

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.83137	0.276
Mature Green Tomato/Ripe Tomato	0.72099	0.165
Immature Eggplant/Mature Eggplant	4.06858	0.05
Ripe Pepper/Ripe Tomato	0.59126	0.224
Mature Eggplant/Ripe Tomato	0.25401	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.93185	0.944
1-1-2/M82	0.99229
12-2/M82	0.87772
12-4/M82	1.22969	0.694
1-3/M82	1.24446
2-1-1/M82	1.31639	0.689
2-1/M82	1.05647	1
2-6/M82	0.99592	1
3-2/M82	N/A	N/A
4-1-1/M82	1.13476	1
4-1/M82	0.74202
4-3-2/M82	N/A	N/A
4-3/M82	0.93833	1
5-3/M82	1.01681	1
6-2/M82	1.53093	1
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.94054	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.46814	0.395
IL7-5/WTpooled	1.15103
IL7-3/WTpooled	0.93204	1
IL12-4/WTpooled	1.6641	0.673
IL1-4/WTpooled	0.90061	0.834
WT/WTpooled	1.06181	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	0.92849	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97069	1
DC3000/delta hrp 6h	0.94058	0.95
DC3000/delta hrp 12h	1.09031	1
DC3000/delta hrp 24h	1.14035	0.535

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.05655
DC3000 delta B/DC3000 delta AB	2.04443

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.99529	1
Exp 36h	0.93205	0.749
Exp 60h	0.98708	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98188	1
Var 0h	1.16294	0.936
Var 12h I row2-row1	0.95891	0.856
Var 12h NI row2-row1	0.84386	0.713
Var 36h I row2-row1	1.17802	0.339
Var 36h NI row2-row1	1.20583	0.482
Var 60h I row2-row1	0.993	1
Var 60h NI row2-row1	1.15686	0.904
Time course 0hI-0hNI	0.99677	1
Time course 12hI-12hNI	1.09604	0.178
Time course 36hI-36hNI	1.54124	0.009
Time course 60hI-60hNI	1.37051	0.025

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)	0.91342	0.301
transgenic ySAMdc/azygous control (breaker)	0.62187	0.15
transgenic ySAMdc/azygous control (red)	1.5592	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.57179	0.036

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.52901	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.90774	1
Manapal/WT (break)	1.17502	0.381
Manapal/WT (red)	1.00975	0.863