Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.4.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.28483	0.523
27DAP/17DAP	0.99907	1
39DAP/27DAP	1.26421	0.4
41DAP/39DAP	0.82864	0.34
42DAP/41DAP	0.98201	1
43DAP/42DAP	1.05161	1
47DAP/43DAP	1.05081	0.825
52DAP/47DAP	1.04359	0.949
57DAP/52DAP	1.06003	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00411	0.824
17DAP/reference	1.16487	0.178
27DAP/reference	0.94647	0.428
39DAP/reference	1.0077	0.903
41DAP/reference	1.07046	0.034
42DAP/reference	0.87503	0.02
43DAP/reference	1.03559	0.705
47DAP/reference	0.92127	0.055
52DAP/reference	0.83257	0.121
57DAP/reference	0.92196	0.277

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99777	0.871
27DAP/17DAP	1.11023	0.458
39DAP/27DAP	1.04054	0.685
41DAP/39DAP	0.97451	0.973
42DAP/41DAP	1.03875	0.773
43DAP/42DAP	0.88441	0.024
47DAP/43DAP	1.06019	0.234
52DAP/47DAP	0.99878	0.979
57DAP/52DAP	0.96543	0.507
57DAP/7DAP	1.06939	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90964	0.157
17DAP/reference	0.89297	0.012
27DAP/reference	0.87819	0.022
39DAP/reference	0.93297	0.015
41DAP/reference	0.87749	0.022
42DAP/reference	0.91524	0.014
43DAP/reference	0.8915	0.016
47DAP/reference	0.97177	0.671
52DAP/reference	0.8413	0.053
57DAP/reference	0.85264	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19639	0.041
17DAP/reference	0.86583	0.253
27DAP/reference	0.83308	0.058
39DAP/reference	0.87454	0.122
41DAP/reference	0.8399	0.118
42DAP/reference	0.81897	0.013
43DAP/reference	0.98206	0.657
47DAP/reference	0.87002	0.017
52DAP/reference	0.91145	0.031
57DAP/reference	0.99295	0.754

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96303	0.119
17DAP/reference	0.96266	0.499
27DAP/reference	0.89483	0.038
39DAP/reference	0.88281	0.026
41DAP/reference	0.9306	0.019
42DAP/reference	0.83997	0.032
43DAP/reference	0.81487	0.073
47DAP/reference	0.88827	0.066
52DAP/reference	0.78033	0.073
57DAP/reference	0.6838	0.023

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9316	1
26DAP/20DAP	1.78028	0.106
34DAP/26DAP	0.89565	0.653
51DAP/34DAP	1.24478	0.081
52DAP/51DAP	0.84552	0.151
53DAP/52DAP	1.07941	0.384
55DAP/53DAP	0.97151	0.796
57DAP/55DAP	1.09665	0.927
62DAP/57DAP	1.22565	0.35
68DAP/62DAP	0.97419	0.863
68DAP/14DAP	1.111	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.7302	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.38528	0.128
Mature Green Tomato/Ripe Tomato	1.07332	0.299
Immature Eggplant/Mature Eggplant	1.61865	0.058
Ripe Pepper/Ripe Tomato	0.97493	1
Mature Eggplant/Ripe Tomato	1.00956	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96929	0.944
1-1-2/M82	0.98625	1
12-2/M82	0.94044	0.955
12-4/M82	1.09422	1
1-3/M82	0.93725	1
2-1-1/M82	1.19861	0.439
2-1/M82	N/A	N/A
2-6/M82	1.14086	0.594
3-2/M82	1.0436	0.967
4-1-1/M82	0.98036	1
4-1/M82	1.1574
4-3-2/M82	0.88142	1
4-3/M82	1.05089
5-3/M82	0.98107	1
6-2/M82	0.93105	1
6-3/M82	0.81003
7-1/M82	1.15406	1
7-2/M82	0.92349	0.796
9-3-2/M82	0.95685	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.94129	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.06019	1
IL12-4/WTpooled	0.78665	0.478
IL1-4/WTpooled	0.91903
WT/WTpooled	1.01584	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	1.06824	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99379	1
DC3000/delta hrp 6h	1.14486	1
DC3000/delta hrp 12h	1.10471	1
DC3000/delta hrp 24h	1.18271	0.103

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.31137	0.042
DC3000 delta B/DC3000 delta AB	1.13096	0.288

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07934	1
Exp 36h	1.55861	0.409
Exp 60h	1.58815	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.05912	0.263
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	0.19574
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.90839	0.377
transgenic ySAMdc/azygous control (breaker)	1.04373	1
transgenic ySAMdc/azygous control (red)	0.94026	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01422	0.213

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.8451	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.0425	1
Manapal/WT (break)	0.90731	1
Manapal/WT (red)	1.02732	1