Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.15.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96813	0.788
27DAP/17DAP	0.98535	1
39DAP/27DAP	1.03922	1
41DAP/39DAP	1.05698	0.921
42DAP/41DAP	1.1467	0.82
43DAP/42DAP	0.9058	0.697
47DAP/43DAP	1.22122	0.809
52DAP/47DAP	1.24724	0.665
57DAP/52DAP	0.97101	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98765	0.63
17DAP/reference	1.04478	0.092
27DAP/reference	0.99928	0.923
39DAP/reference	0.9707	0.587
41DAP/reference	0.95192	0.434
42DAP/reference	0.94371	0.052
43DAP/reference	0.9832	0.728
47DAP/reference	0.89467	0.042
52DAP/reference	0.83148	0.089
57DAP/reference	0.80171	0.047

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99182	0.801
27DAP/17DAP	0.98279	0.887
39DAP/27DAP	1.04365	0.677
41DAP/39DAP	1.00825	1
42DAP/41DAP	1.03932	0.886
43DAP/42DAP	1.04929	0.554
47DAP/43DAP	1.01448	1
52DAP/47DAP	0.98126	0.913
57DAP/52DAP	0.91691	0.328
57DAP/7DAP	1.16956	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91731	0.091
17DAP/reference	0.97569	0.295
27DAP/reference	0.95611	0.028
39DAP/reference	0.96094	0.109
41DAP/reference	0.98147	0.489
42DAP/reference	0.97864	0.248
43DAP/reference	0.922	0.033
47DAP/reference	1.01806	0.948
52DAP/reference	1.0121	0.886
57DAP/reference	0.94611	0.03

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99242	0.848
17DAP/reference	0.96526	0.389
27DAP/reference	0.88628	0.144
39DAP/reference	0.87455	0.095
41DAP/reference	0.90601	0.164
42DAP/reference	1.01321	1
43DAP/reference	1.02272	0.89
47DAP/reference	1.07998	0.366
52DAP/reference	0.97204	0.327
57DAP/reference	1.13854	0.035

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97979	0.566
17DAP/reference	1.00061	0.918
27DAP/reference	0.89658	0.031
39DAP/reference	0.89865	0.01
41DAP/reference	0.92464	0.043
42DAP/reference	0.89911	0.059
43DAP/reference	0.86972	0.044
47DAP/reference	0.99685	0.687
52DAP/reference	0.87293	0.139
57DAP/reference	0.81356	0.092

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04762	0.878
26DAP/20DAP	0.90596	1
34DAP/26DAP	0.87236	0.702
51DAP/34DAP	0.90609	0.41
52DAP/51DAP	1.06195	0.606
53DAP/52DAP	0.87476	0.17
55DAP/53DAP	0.87517	0.389
57DAP/55DAP	1.07347	0.793
62DAP/57DAP	1.13391	0.393
68DAP/62DAP	1.0358	1
68DAP/14DAP	0.93993	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.79145	0.211

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.07864	0.814
Immature Eggplant/Mature Eggplant	1.07828	0.215
Ripe Pepper/Ripe Tomato	0.69029
Mature Eggplant/Ripe Tomato	1.13324

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.34321	1
1-1-2/M82	0.6924	0.958
12-2/M82	1.19736	1
12-4/M82	0.89976	1
1-3/M82	1.58902	1
2-1-1/M82	1.92002	1
2-1/M82	2.76105	1
2-6/M82	1.07208	0.505
3-2/M82	0.93953	1
4-1-1/M82	1.72897	1
4-1/M82	1.14572	1
4-3-2/M82	0.78938	1
4-3/M82	1.51014	1
5-3/M82	0.82427	1
6-2/M82	1.17294	1
6-3/M82	1.06968	1
7-1/M82	1.01941	1
7-2/M82	1.18761	1
9-3-2/M82	0.89933	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.0197	1
IL2-6/WTpooled	0.92618	1
IL7-5/WTpooled	0.66573	1
IL7-3/WTpooled	1.07659	1
IL12-4/WTpooled	0.93931	0.71
IL1-4/WTpooled	1.04287	1
WT/WTpooled	1.01594	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	0.98492	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.13984	0.921
DC3000/delta hrp 6h	0.85856	0.95
DC3000/delta hrp 12h	1.24002	1
DC3000/delta hrp 24h	1.28481	0.567

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.02969	0.515
DC3000 delta B/DC3000 delta AB	0.97177	0.745

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.40197	1
Exp 36h	1.31516	0.693
Exp 60h	1.37818	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98233	1
Var 0h	0.94288	1
Var 12h I row2-row1	1.06168	0.296
Var 12h NI row2-row1	0.94543	0.82
Var 36h I row2-row1	0.94822	1
Var 36h NI row2-row1	0.91558	0.522
Var 60h I row2-row1	1.38789	0.562
Var 60h NI row2-row1	1.15971	0.904
Time course 0hI-0hNI	1.04335	0.852
Time course 12hI-12hNI	1.06302	0.63
Time course 36hI-36hNI	1.01495	0.799
Time course 60hI-60hNI	1.079	0.359

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)	0.8868	0.314
transgenic ySAMdc/azygous control (breaker)	1.11965	0.248
transgenic ySAMdc/azygous control (red)	0.94507	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0256	0.35

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.03532	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.96004	1
Manapal/WT (break)	0.85496	1
Manapal/WT (red)	1.42957	0.137