Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.7.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.49282	0.138
27DAP/17DAP	0.69975	0.201
39DAP/27DAP	0.78587	0.41
41DAP/39DAP	0.77423	0.213
42DAP/41DAP	1.03143	1
43DAP/42DAP	1.03946	1
47DAP/43DAP	0.36639	0.049
52DAP/47DAP	0.89555	0.716
57DAP/52DAP	1.78228	0.95

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06544	0.303
17DAP/reference	1.03188	0.546
27DAP/reference	0.86503	0.013
39DAP/reference	0.88763	0.023
41DAP/reference	0.93139	0.018
42DAP/reference	0.92143	0.02
43DAP/reference	0.869	0.018
47DAP/reference	0.86589	0.021
52DAP/reference	0.80908	0.025
57DAP/reference	0.82634	0.031

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.42063	0.058
27DAP/17DAP	0.80497	0.227
39DAP/27DAP	0.69005	0.094
41DAP/39DAP	2.28288	0.008
42DAP/41DAP	0.69285	0.01
43DAP/42DAP	0.55833	0.022
47DAP/43DAP	0.92429	0.395
52DAP/47DAP	1.1157	0.756
57DAP/52DAP	0.70188	0.177
57DAP/7DAP	0.63014	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92575	0.326
17DAP/reference	0.96044	0.447
27DAP/reference	1.20402	0.246
39DAP/reference	0.87988	0.083
41DAP/reference	0.95791	0.449
42DAP/reference	0.83043	0.033
43DAP/reference	0.79465	0.027
47DAP/reference	0.9435	0.504
52DAP/reference	1.0993	0.684
57DAP/reference	0.96336	0.396

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11158	0.246
17DAP/reference	1.3876	0.012
27DAP/reference	1.28148	0.054
39DAP/reference	1.18621	0.2
41DAP/reference	1.08433	0.925
42DAP/reference	0.93709	0.289
43DAP/reference	1.09538	0.745
47DAP/reference	0.87747	0.042
52DAP/reference	0.98467	0.5
57DAP/reference	0.87891	0.058

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97593	0.566
17DAP/reference	1.50715	0.105
27DAP/reference	1.04736	0.805
39DAP/reference	1.10631	0.211
41DAP/reference	0.96998	0.56
42DAP/reference	1.09856	0.671
43DAP/reference	1.32067	0.081
47DAP/reference	0.90415	0.038
52DAP/reference	0.88739	0.289
57DAP/reference	1.54132	0.064

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95154	1
26DAP/20DAP	0.76493	0.512
34DAP/26DAP	0.89038	0.675
51DAP/34DAP	0.82477	0.158
52DAP/51DAP	1.04246	0.965
53DAP/52DAP	0.98211	0.902
55DAP/53DAP	1.24017	0.319
57DAP/55DAP	1.05926	0.906
62DAP/57DAP	0.98941	0.994
68DAP/62DAP	0.90308	0.747
68DAP/14DAP	0.6925	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.43462	0.099

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.27377	0.058
Mature Green Tomato/Ripe Tomato	15.2727	0.015
Immature Eggplant/Mature Eggplant	0.58128	0.072
Ripe Pepper/Ripe Tomato	1.43666	1
Mature Eggplant/Ripe Tomato	8.86127

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
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	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.04427	0.891
IL1-4/WTpooled	1.09035
WT/WTpooled	0.89583	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	1.10608	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.90712	1
DC3000/delta hrp 6h	1.04702	1
DC3000/delta hrp 12h	1.355	1
DC3000/delta hrp 24h	0.66087	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.70938	0.11
DC3000 delta B/DC3000 delta AB	0.71282	0.04

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.92434	1
Exp 36h	0.85622	0.449
Exp 60h	0.87762	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95623	1
Var 0h	1.01494	1
Var 12h I row2-row1	0.81616	0.353
Var 12h NI row2-row1	1.04455	1
Var 36h I row2-row1	1.14824	0.742
Var 36h NI row2-row1	0.69261	0.522
Var 60h I row2-row1	0.96441	0.952
Var 60h NI row2-row1	0.90447	0.932
Time course 0hI-0hNI	1.01889	0.867
Time course 12hI-12hNI	1.00642	0.888
Time course 36hI-36hNI	1.3565	0.006
Time course 60hI-60hNI	1.73325	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)	1.19372	0.654
transgenic ySAMdc/azygous control (breaker)	3.33525	0.162
transgenic ySAMdc/azygous control (red)	0.96709	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.80578	0.143

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.69254	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	6.36455	0.088
Manapal/WT (break)	7.65478	0.126
Manapal/WT (red)	4.69349	0.164