Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.1.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86917	0.381
27DAP/17DAP	1.21415	0.783
39DAP/27DAP	1.03614	0.857
41DAP/39DAP	1.17645	0.58
42DAP/41DAP	0.95621	1
43DAP/42DAP	0.85277	0.71
47DAP/43DAP	0.91242	0.696
52DAP/47DAP	1.87621	0.292
57DAP/52DAP	0.70687	0.681

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10426	0.179
17DAP/reference	0.97858	0.701
27DAP/reference	0.90172	0.265
39DAP/reference	1.11365	0.162
41DAP/reference	0.98348	0.814
42DAP/reference	1.12847	0.02
43DAP/reference	1.06986	0.306
47DAP/reference	1.12014	0.031
52DAP/reference	1.05737	0.102
57DAP/reference	1.14004	0.31

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01554	1
27DAP/17DAP	0.99243	0.943
39DAP/27DAP	1.08073	0.611
41DAP/39DAP	1.07786	0.663
42DAP/41DAP	0.9791	0.743
43DAP/42DAP	1.02142	1
47DAP/43DAP	1.0049	0.998
52DAP/47DAP	1.00818	0.975
57DAP/52DAP	0.98941	0.813
57DAP/7DAP	1.07175

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97395	0.495
17DAP/reference	1.031	0.361
27DAP/reference	1.23628	0.018
39DAP/reference	0.91954	0.083
41DAP/reference	1.04247	0.56
42DAP/reference	1.06469	0.233
43DAP/reference	1.01354	1
47DAP/reference	1.0479	0.761
52DAP/reference	0.9204	0.163
57DAP/reference	0.8739	0.086

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13113	0.07
17DAP/reference	1.12191	0.426
27DAP/reference	1.35355	0.053
39DAP/reference	1.50372	0.063
41DAP/reference	1.3342	0.041
42DAP/reference	1.34516	0.03
43DAP/reference	1.6359	0.012
47DAP/reference	1.22087	0.232
52DAP/reference	1.17467	0.596
57DAP/reference	1.37605	0.14

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9378	0.098
17DAP/reference	1.07042	0.665
27DAP/reference	0.87638	0.126
39DAP/reference	0.92326	0.179
41DAP/reference	1.04667	0.521
42DAP/reference	1.46841	0.036
43DAP/reference	1.27923	0.291
47DAP/reference	1.25758	0.053
52DAP/reference	1.18027	0.119
57DAP/reference	1.81521	0.015

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.53364	0.966
26DAP/20DAP	1.07453	0.798
34DAP/26DAP	1.02732	1
51DAP/34DAP	1.03588	0.925
52DAP/51DAP	1.05834	0.821
53DAP/52DAP	0.97978	0.868
55DAP/53DAP	1.18074	0.494
57DAP/55DAP	1.03249	0.997
62DAP/57DAP	1.33931	0.833
68DAP/62DAP	1.03838	1
68DAP/14DAP	1.7143	0.053

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.42569	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.78785	0.265
Mature Green Tomato/Ripe Tomato	1.00444	0.835
Immature Eggplant/Mature Eggplant	0.82337	0.125
Ripe Pepper/Ripe Tomato	1.13284	1
Mature Eggplant/Ripe Tomato	1.05147	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.07114	1
1-1-2/M82	1.0808	1
12-2/M82	1.25763	1
12-4/M82	0.91659	1
1-3/M82	1.09502	0.479
2-1-1/M82	0.9435	1
2-1/M82	0.70142
2-6/M82	1.13941	0.329
3-2/M82	0.96107	0.455
4-1-1/M82	0.83628	1
4-1/M82	1.06357	1
4-3-2/M82	1.01228	1
4-3/M82	0.86738	0.72
5-3/M82	0.99185	1
6-2/M82	0.85618	0.497
6-3/M82	0.97509	1
7-1/M82	0.9813	1
7-2/M82	1.02542	1
9-3-2/M82	0.90788	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.1944
IL2-6/WTpooled	1.47893	0.584
IL7-5/WTpooled	0.97256	1
IL7-3/WTpooled	0.9645	1
IL12-4/WTpooled	0.7948	0.566
IL1-4/WTpooled	0.96118	1
WT/WTpooled	0.9075	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	0.90797	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.133	0.724
DC3000/delta hrp 6h	0.97028	0.95
DC3000/delta hrp 12h	1.0116	1
DC3000/delta hrp 24h	1.02984	0.728

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.90072
DC3000 delta B/DC3000 delta AB	1.09263	0.472

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98724	1
Exp 36h	1.08698	1
Exp 60h	1.1644	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98561	1
Var 0h	1.4839	0.98
Var 12h I row2-row1	1.0773	0.58
Var 12h NI row2-row1	0.82872	0.627
Var 36h I row2-row1	1.03342	1
Var 36h NI row2-row1	1.02625	1
Var 60h I row2-row1	1.12359	0.543
Var 60h NI row2-row1	0.94674	0.977
Time course 0hI-0hNI	1.00497	1
Time course 12hI-12hNI	1.01913	0.786
Time course 36hI-36hNI	1.06071	0.248
Time course 60hI-60hNI	1.11038	0.216

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)	0.99022	0.789
transgenic ySAMdc/azygous control (breaker)	1.13142	1
transgenic ySAMdc/azygous control (red)	1.0498	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08135	0.04

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.90894	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.9395	1
Manapal/WT (break)	0.94578	0.333
Manapal/WT (red)	1.07718	1