Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.17.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.69143	0.078
27DAP/17DAP	1.16712	0.845
39DAP/27DAP	1.21112	0.759
41DAP/39DAP	1.47239	0.511
42DAP/41DAP	1.56827	0.232
43DAP/42DAP	0.96462	0.906
47DAP/43DAP	0.68701	0.137
52DAP/47DAP	1.15193	0.772
57DAP/52DAP	1.31582	0.849

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79319	0.094
17DAP/reference	0.65795	0.007
27DAP/reference	1.0429	0.923
39DAP/reference	0.75292	0.027
41DAP/reference	0.62982	0.008
42DAP/reference	0.97338	0.326
43DAP/reference	0.96908	0.594
47DAP/reference	1.13191	0.524
52DAP/reference	1.54339	0.011
57DAP/reference	1.45912	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00287	0.847
27DAP/17DAP	1.221	0.274
39DAP/27DAP	1.47694	0.066
41DAP/39DAP	0.88839	0.567
42DAP/41DAP	1.29283	0.009
43DAP/42DAP	1.24117	0.04
47DAP/43DAP	0.92102	0.457
52DAP/47DAP	0.96062	0.837
57DAP/52DAP	0.79705	0.062
57DAP/7DAP	1.18514	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07504	0.491
17DAP/reference	0.95854	0.338
27DAP/reference	1.01055	1
39DAP/reference	1.07173	0.779
41DAP/reference	1.12234	0.207
42DAP/reference	1.14412	0.308
43DAP/reference	1.43099	0.014
47DAP/reference	1.30659	0.115
52DAP/reference	1.12786	0.183
57DAP/reference	0.90009	0.038

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81463	0.152
17DAP/reference	0.63901	0.003
27DAP/reference	0.85336	0.173
39DAP/reference	0.91115	0.156
41DAP/reference	1.04879	0.893
42DAP/reference	0.98286	0.534
43DAP/reference	0.73937	0.032
47DAP/reference	0.87578	0.066
52DAP/reference	0.80949	0.01
57DAP/reference	0.62321	0.006

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03456	0.846
17DAP/reference	0.86748	0.214
27DAP/reference	1.11963	0.312
39DAP/reference	0.99892	0.819
41DAP/reference	0.97891	0.618
42DAP/reference	1.39704	0.034
43DAP/reference	1.1922	0.157
47DAP/reference	1.08383	0.501
52DAP/reference	1.32487	0.201
57DAP/reference	1.4608	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.17491	0.966
26DAP/20DAP	2.19333	0.097
34DAP/26DAP	0.79867	0.728
51DAP/34DAP	1.22137	0.988
52DAP/51DAP	0.73518	1
53DAP/52DAP	1.15715	0.688
55DAP/53DAP	1.3742	0.712
57DAP/55DAP	0.92059	0.688
62DAP/57DAP	0.88038	0.681
68DAP/62DAP	2.76175	0.005
68DAP/14DAP	2.57458	0.023

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	7.21286	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.88666	0.401
Mature Green Tomato/Ripe Tomato	0.72393	0.2
Immature Eggplant/Mature Eggplant	1.44145	0.05
Ripe Pepper/Ripe Tomato	0.64243	0.224
Mature Eggplant/Ripe Tomato	0.93056	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04643	1
1-1-2/M82	1.17809	1
12-2/M82	0.76688
12-4/M82	0.9613	0.619
1-3/M82	N/A	N/A
2-1-1/M82	1.15221	0.457
2-1/M82	0.84639
2-6/M82	1.13589
3-2/M82	1.57416
4-1-1/M82	1.08387
4-1/M82	1.24147	1
4-3-2/M82	2.11793	0.241
4-3/M82	1.79774	0.268
5-3/M82	0.84	1
6-2/M82	N/A	N/A
6-3/M82	0.61057	0.619
7-1/M82	0.86027	0.408
7-2/M82	1.37893	0.324
9-3-2/M82	1.4645	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.21723	0.361
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.15815	1
IL12-4/WTpooled	0.7751	0.71
IL1-4/WTpooled	1.09918	1
WT/WTpooled	1.06723	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	1.25728	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0671	0.921
DC3000/delta hrp 6h	0.77344	0.95
DC3000/delta hrp 12h	1.04355	1
DC3000/delta hrp 24h	1.99374	0.03

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.41854	0.046
DC3000 delta B/DC3000 delta AB	1.59632	0.081

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04263	1
Exp 36h	1.36291	0.693
Exp 60h	1.29501	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98091	1
Var 0h	1.01528	1
Var 12h I row2-row1	1.04015	0.795
Var 12h NI row2-row1	1.49883	0.16
Var 36h I row2-row1	1.16644	1
Var 36h NI row2-row1	1.10143	1
Var 60h I row2-row1	0.86015	0.439
Var 60h NI row2-row1	1.12352	1
Time course 0hI-0hNI	0.88936	0.352
Time course 12hI-12hNI	1.17012	0.035
Time course 36hI-36hNI	2.1926	0.005
Time course 60hI-60hNI	5.79842	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)	1.00404	1
transgenic ySAMdc/azygous control (breaker)	1.36354	0.162
transgenic ySAMdc/azygous control (red)	1.11926	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.58261	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.84175	1
Manapal/WT (break)	0.72241	0.333
Manapal/WT (red)	0.83832	0.188