Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.7.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86125	0.31
27DAP/17DAP	1.15953	0.825
39DAP/27DAP	1.29235	0.603
41DAP/39DAP	1.0332	0.934
42DAP/41DAP	0.81329	0.774
43DAP/42DAP	1.10333	1
47DAP/43DAP	0.95759	0.825
52DAP/47DAP	1.13708	0.818
57DAP/52DAP	1.14459	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87282	0.177
17DAP/reference	0.73294	0.007
27DAP/reference	0.96636	0.552
39DAP/reference	0.92691	0.292
41DAP/reference	0.80695	0.026
42DAP/reference	0.95287	0.242
43DAP/reference	0.87776	0.042
47DAP/reference	0.96663	0.366
52DAP/reference	1.24976	0.186
57DAP/reference	1.36196	0.012

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88515	0.148
27DAP/17DAP	1.03511	0.938
39DAP/27DAP	0.98224	0.887
41DAP/39DAP	1.20283	0.183
42DAP/41DAP	0.94207	0.466
43DAP/42DAP	0.88636	0.06
47DAP/43DAP	1.00132	1
52DAP/47DAP	1.04021	0.986
57DAP/52DAP	1.05611	0.895
57DAP/7DAP	0.91031	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83066	0.129
17DAP/reference	0.88778	0.028
27DAP/reference	0.90788	0.03
39DAP/reference	0.74195	0.013
41DAP/reference	0.95745	0.298
42DAP/reference	0.99554	0.675
43DAP/reference	0.86045	0.032
47DAP/reference	0.99061	1
52DAP/reference	0.95702	0.304
57DAP/reference	0.81418	0.013

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.72596	0.015
17DAP/reference	0.75807	0.015
27DAP/reference	1.19455	0.095
39DAP/reference	1.13442	0.335
41DAP/reference	1.00699	0.615
42DAP/reference	1.04563	0.794
43DAP/reference	0.97152	0.507
47DAP/reference	0.8812	0.04
52DAP/reference	0.98032	0.576
57DAP/reference	0.77833	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88845	0.082
17DAP/reference	1.00047	0.778
27DAP/reference	0.94492	0.376
39DAP/reference	1.00428	1
41DAP/reference	1.08414	0.818
42DAP/reference	1.39572	0.103
43DAP/reference	1.38058	0.202
47DAP/reference	0.94213	0.357
52DAP/reference	0.80746	0.121
57DAP/reference	1.67245	0.021

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10111	0.966
26DAP/20DAP	1.06825	1
34DAP/26DAP	1.18585	0.819
51DAP/34DAP	0.97424	0.758
52DAP/51DAP	0.95217	1
53DAP/52DAP	1.01064	1
55DAP/53DAP	1.08713	0.782
57DAP/55DAP	1.03881	0.927
62DAP/57DAP	0.83628	0.871
68DAP/62DAP	1.83513	0.153
68DAP/14DAP	1.97447	0.022

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.21199	0.047

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.6967	0.204
Mature Green Tomato/Ripe Tomato	1.3254	0.437
Immature Eggplant/Mature Eggplant	1.00766	1
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.65468	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04134	0.877
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.23456	0.611
1-3/M82	0.79009
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.85171	1
3-2/M82	0.97741
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	1.06818	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.5958
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	1.11667	0.584
IL7-5/WTpooled	0.95755	1
IL7-3/WTpooled	0.77347
IL12-4/WTpooled	1.12753	0.839
IL1-4/WTpooled	0.9222	0.562
WT/WTpooled	0.99179	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	0.98488	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05972	0.921
DC3000/delta hrp 6h	1.18985	1
DC3000/delta hrp 12h	0.93096	1
DC3000/delta hrp 24h	0.93359	0.575

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.6716	0.053
DC3000 delta B/DC3000 delta AB	0.97331	0.873

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	0.98319	1
Var 0h	0.97902	1
Var 12h I row2-row1	1.02296	0.736
Var 12h NI row2-row1	0.92232	0.82
Var 36h I row2-row1	0.878	1
Var 36h NI row2-row1	0.9334	0.329
Var 60h I row2-row1	0.95807	0.832
Var 60h NI row2-row1	0.8895	0.866
Time course 0hI-0hNI	0.9979	1
Time course 12hI-12hNI	1.03508	0.687
Time course 36hI-36hNI	1.10654	0.063
Time course 60hI-60hNI	1.26213	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)	1.20997	0.326
transgenic ySAMdc/azygous control (breaker)	1.02308	1
transgenic ySAMdc/azygous control (red)	1.03369	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03436	0.089

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.96484	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.20204	0.307
Manapal/WT (break)	1.27032	0.381
Manapal/WT (red)	1.05442	1