Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.4.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	5.38281	0.05
27DAP/17DAP	0.58894	0.088
39DAP/27DAP	0.78829	0.353
41DAP/39DAP	1.00708	1
42DAP/41DAP	1.67403	0.029
43DAP/42DAP	0.77313	0.543
47DAP/43DAP	0.58597	0.072
52DAP/47DAP	0.81306	0.572
57DAP/52DAP	1.01124	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98076	0.578
17DAP/reference	0.70398	0.021
27DAP/reference	0.79122	0.011
39DAP/reference	0.90488	0.437
41DAP/reference	1.07021	0.338
42DAP/reference	0.79977	0.008
43DAP/reference	0.88843	0.576
47DAP/reference	0.83137	0.032
52DAP/reference	0.82895	0.21
57DAP/reference	1.03735

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00996	0.871
27DAP/17DAP	1.31104	0.122
39DAP/27DAP	0.48931	0.028
41DAP/39DAP	1.57706	0.018
42DAP/41DAP	0.84812	0.118
43DAP/42DAP	0.75861	0.028
47DAP/43DAP	0.88956	0.098
52DAP/47DAP	1.00893	0.925
57DAP/52DAP	0.68576	0.156
57DAP/7DAP	0.8013	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17257	0.235
17DAP/reference	1.10512	0.134
27DAP/reference	1.11518	0.551
39DAP/reference	1.47182	0.01
41DAP/reference	1.04687	0.836
42DAP/reference	1.14019	0.308
43DAP/reference	0.77241	0.019
47DAP/reference	0.80237	0.222
52DAP/reference	0.79691	0.066
57DAP/reference	0.79177	0.037

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82768	0.134
17DAP/reference	0.78544	0.029
27DAP/reference	0.82281	0.22
39DAP/reference	1.29443	0.019
41DAP/reference	0.94238	0.226
42DAP/reference	1.11147	0.288
43DAP/reference	0.77188	0.028
47DAP/reference	1.05185	0.712
52DAP/reference	0.97364	0.433
57DAP/reference	0.89886	0.338

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16796	0.338
17DAP/reference	0.94585	0.519
27DAP/reference	0.95972	0.357
39DAP/reference	0.87383	0.101
41DAP/reference	1.20041	0.257
42DAP/reference	0.99943	1
43DAP/reference	0.91211	0.226
47DAP/reference	0.64848	0.006
52DAP/reference	0.70803	0.098
57DAP/reference	0.88224	0.09

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07506	1
26DAP/20DAP	0.5659	0.112
34DAP/26DAP	0.91511
51DAP/34DAP	1.77671	0.098
52DAP/51DAP	0.97098	1
53DAP/52DAP	1.03042	1
55DAP/53DAP	0.93815	0.735
57DAP/55DAP	1.10651	0.927
62DAP/57DAP	0.95063	1
68DAP/62DAP	1.61552	0.21
68DAP/14DAP	1.53969	0.026

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.03879	0.038

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	11.6627	0.016
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.4359

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.23662	0.877
1-1-2/M82	1.15294	0.977
12-2/M82	0.70705	0.955
12-4/M82	0.8076	0.298
1-3/M82	1.1272	1
2-1-1/M82	1.1145	1
2-1/M82	1.13056	1
2-6/M82	0.49272	0.501
3-2/M82	1.11958	0.967
4-1-1/M82	1.14785	1
4-1/M82	1.36864
4-3-2/M82	1.10861
4-3/M82	0.36894	0.475
5-3/M82	2.19299	0.572
6-2/M82	0.49342	0.481
6-3/M82	1.1274	1
7-1/M82	1.18529
7-2/M82	0.60396	0.486
9-3-2/M82	1.20344

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.16641	0.365
IL2-6/WTpooled	0.67877	1
IL7-5/WTpooled	1.03906
IL7-3/WTpooled	1.40526	1
IL12-4/WTpooled	0.89377	0.71
IL1-4/WTpooled	0.87053	0.562
WT/WTpooled	0.92872	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	1.07018	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.82246	0.571
DC3000/delta hrp 6h	1.105	1
DC3000/delta hrp 12h	1.19976	1
DC3000/delta hrp 24h	0.64711	0.04

Experiment: DC3000 effector mutants

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

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98764	1
Var 0h	2.11247	0.98
Var 12h I row2-row1	0.83319	0.627
Var 12h NI row2-row1	0.9811	0.906
Var 36h I row2-row1	0.78819	1
Var 36h NI row2-row1	1.27068	0.253
Var 60h I row2-row1	1.05773
Var 60h NI row2-row1	1.06121	1
Time course 0hI-0hNI	0.99912	1
Time course 12hI-12hNI	0.95558	0.618
Time course 36hI-36hNI	0.93862	0.344
Time course 60hI-60hNI	0.1128	0.005

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)	1.44853	0.283
transgenic ySAMdc/azygous control (breaker)	0.86718	0.49
transgenic ySAMdc/azygous control (red)	1.16942	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00106	1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.89103	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.41996	1
Manapal/WT (break)	0.50515	1
Manapal/WT (red)	0.67993	0.242