Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.8.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91667	0.578
27DAP/17DAP	1.0624	0.872
39DAP/27DAP	0.98914	0.782
41DAP/39DAP	1.01937	0.96
42DAP/41DAP	0.9926	1
43DAP/42DAP	1.05369	1
47DAP/43DAP	1.07547	0.595
52DAP/47DAP	0.8626	0.622
57DAP/52DAP	1.04233	0.96

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88892	0.238
17DAP/reference	0.72839	0.028
27DAP/reference	0.75145	0.043
39DAP/reference	1.31559	0.434
41DAP/reference	0.97056	0.667
42DAP/reference	0.96954	0.326
43DAP/reference	1.38365	0.019
47DAP/reference	1.50326	0.001
52DAP/reference	1.33694	0.102
57DAP/reference	1.72097	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99651	0.801
27DAP/17DAP	1.0176	0.967
39DAP/27DAP	1.19004	0.151
41DAP/39DAP	0.82458	0.276
42DAP/41DAP	1.13666	0.508
43DAP/42DAP	1.36328	0.026
47DAP/43DAP	1.06803	0.735
52DAP/47DAP	0.85205	0.247
57DAP/52DAP	0.79806	0.121
57DAP/7DAP	1.10964	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68753	0.071
17DAP/reference	0.6377	0.011
27DAP/reference	0.76077	0.028
39DAP/reference	0.69371	0.011
41DAP/reference	1.1429	0.126
42DAP/reference	1.57517	0.03
43DAP/reference	1.61928	0.007
47DAP/reference	1.84959	0.033
52DAP/reference	0.75833	0.012
57DAP/reference	0.74662	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88253	0.329
17DAP/reference	0.57673	0.005
27DAP/reference	0.86052	0.1
39DAP/reference	0.95321	0.221
41DAP/reference	0.75142	0.074
42DAP/reference	0.70288	0.024
43DAP/reference	0.88582	0.277
47DAP/reference	1.14107	0.994
52DAP/reference	0.56674	0.027
57DAP/reference	0.96288	0.549

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.65011	0.046
17DAP/reference	0.68727	0.172
27DAP/reference	0.62989	0.031
39DAP/reference	0.71576	0.019
41DAP/reference	0.60523	0.046
42DAP/reference	1.1322	0.416
43DAP/reference	1.28122	0.362
47DAP/reference	0.69874	0.024
52DAP/reference	0.95753	0.596
57DAP/reference	0.84079	0.138

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.21341	0.966
26DAP/20DAP	1.05913	0.941
34DAP/26DAP	1.00209	1
51DAP/34DAP	1.47068	0.047
52DAP/51DAP	0.68646	0.07
53DAP/52DAP	1.33844	0.08
55DAP/53DAP	0.93411	0.619
57DAP/55DAP	1.26122	0.818
62DAP/57DAP	0.83521	0.466
68DAP/62DAP	1.22117	0.707
68DAP/14DAP	1.51532	0.249

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.0807	0.022

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.14762	0.05
Mature Green Tomato/Ripe Tomato	0.74552	0.055
Immature Eggplant/Mature Eggplant	7.95316	0.05
Ripe Pepper/Ripe Tomato	1.17283	1
Mature Eggplant/Ripe Tomato	0.12332	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06361	0.877
1-1-2/M82	1.28071	0.977
12-2/M82	1.82822	1
12-4/M82	1.03949	1
1-3/M82	2.56626	0.248
2-1-1/M82	1.00559	1
2-1/M82	0.88763	0.74
2-6/M82	0.65925	1
3-2/M82	1.44353
4-1-1/M82	0.82492	1
4-1/M82	1.367	1
4-3-2/M82	1.31052	0.508
4-3/M82	1.29643	1
5-3/M82	0.83872	1
6-2/M82	0.88453
6-3/M82	0.51484	0.916
7-1/M82	0.78611	1
7-2/M82	1.36547	0.324
9-3-2/M82	1.23942	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.94009	0.348
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.00664
IL12-4/WTpooled	0.82179	0.71
IL1-4/WTpooled	1.09407	1
WT/WTpooled	1.228	0.777

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	1.189	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.23764	0.921
DC3000/delta hrp 6h	0.95807	0.95
DC3000/delta hrp 12h	0.78279	1
DC3000/delta hrp 24h	1.82006	0.05

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.89497	0.413
DC3000 delta B/DC3000 delta AB	1.11146	0.345

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.5588	0.228
Exp 36h	1.73892	0.326
Exp 60h	1.59744	0.221

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98543	1
Var 0h	1.14082	0.98
Var 12h I row2-row1	1.12531	0.692
Var 12h NI row2-row1	0.98868	1
Var 36h I row2-row1	0.97622	1
Var 36h NI row2-row1	0.89838	0.522
Var 60h I row2-row1	0.82936	0.285
Var 60h NI row2-row1	0.9218	0.866
Time course 0hI-0hNI	0.99375	1
Time course 12hI-12hNI	1.1697	0.048
Time course 36hI-36hNI	2.18367	0.006
Time course 60hI-60hNI	2.85848	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)	0.77795	0.3
transgenic ySAMdc/azygous control (breaker)	1.9751	0.172
transgenic ySAMdc/azygous control (red)	2.17683	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	2.27605	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95226	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.99225	1
Manapal/WT (break)	1.43458	0.381
Manapal/WT (red)	0.74672	0.181