Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.4.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.54235	0.014
27DAP/17DAP	0.67262	0.149
39DAP/27DAP	0.71565	0.522
41DAP/39DAP	0.6935	0.132
42DAP/41DAP	0.82777	0.774
43DAP/42DAP	1.38431	0.252
47DAP/43DAP	0.66625	0.121
52DAP/47DAP	0.72801	0.247
57DAP/52DAP	0.92189	0.92

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26273	0.032
17DAP/reference	1.08328	0.696
27DAP/reference	1.04881	0.612
39DAP/reference	0.82341	0.015
41DAP/reference	0.89062
42DAP/reference	0.85514	0.035
43DAP/reference	N/A	N/A
47DAP/reference	0.76778	0.002
52DAP/reference	0.71472	0.139
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.77547	0.135
27DAP/17DAP	0.90236	0.537
39DAP/27DAP	0.83794	0.046
41DAP/39DAP	0.72856	0.019
42DAP/41DAP	1.03758	0.947
43DAP/42DAP	1.05991	0.446
47DAP/43DAP	0.89926	0.418
52DAP/47DAP	0.92786	0.763
57DAP/52DAP	0.93297	0.598
57DAP/7DAP	0.58981	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.71154	0.024
17DAP/reference	1.21093	0.025
27DAP/reference	0.90669	0.03
39DAP/reference	0.92672	0.095
41DAP/reference	0.78298	0.015
42DAP/reference	0.82514	0.01
43DAP/reference	0.9331	0.202
47DAP/reference	0.77881	0.066
52DAP/reference	0.75767	0.011
57DAP/reference	0.94635	0.232

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29915	0.172
17DAP/reference	1.1252	0.278
27DAP/reference	0.98697	0.642
39DAP/reference	0.82712	0.031
41DAP/reference	0.96047	0.268
42DAP/reference	0.82432	0.055
43DAP/reference	0.72883	0.024
47DAP/reference	0.79954	0.026
52DAP/reference	0.90112	0.143
57DAP/reference	0.94506	0.408

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.64383	0.017
17DAP/reference	1.34811	0.126
27DAP/reference	1.13733	0.067
39DAP/reference	1.01535	0.962
41DAP/reference	0.96558	0.512
42DAP/reference	0.91102	0.552
43DAP/reference	0.97469	0.66
47DAP/reference	0.70873	0.005
52DAP/reference	0.61922	0.064
57DAP/reference	0.73407	0.04

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02986	1
26DAP/20DAP	1.31698	0.312
34DAP/26DAP	1.2228	0.304
51DAP/34DAP	0.79347	0.098
52DAP/51DAP	1.02912	0.836
53DAP/52DAP	0.80552	0.27
55DAP/53DAP	0.9655	0.746
57DAP/55DAP	1.04882	0.881
62DAP/57DAP	1.18687	0.833
68DAP/62DAP	0.94093	0.769
68DAP/14DAP	0.71827	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.31023	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	5.34748	0.058
Mature Green Tomato/Ripe Tomato	15.5842	0.015
Immature Eggplant/Mature Eggplant	0.27137	0.057
Ripe Pepper/Ripe Tomato	16.34	0.256
Mature Eggplant/Ripe Tomato	93.3166	0.26

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	1.20507	0.365
IL2-6/WTpooled	1.27688	0.395
IL7-5/WTpooled	1.33738	1
IL7-3/WTpooled	0.71624
IL12-4/WTpooled	1.24001	0.737
IL1-4/WTpooled	0.88948	0.699
WT/WTpooled	1.01783	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	0.85699	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08129	0.921
DC3000/delta hrp 6h	1.00177	0.95
DC3000/delta hrp 12h	1.22667	1
DC3000/delta hrp 24h	0.34297	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.39879	0.023
DC3000 delta B/DC3000 delta AB	0.42257	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9937	1
Exp 36h	0.76393	0.471
Exp 60h	0.60643	0.278

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

hybridization	ratio	FDR (corrected p value)
self-self	1.09719	1
Var 0h	1.19241	1
Var 12h I row2-row1	0.89573	0.31
Var 12h NI row2-row1	0.99473	1
Var 36h I row2-row1	0.83596	0.805
Var 36h NI row2-row1	1.17876	1
Var 60h I row2-row1	1.24044
Var 60h NI row2-row1	1.2166	0.904
Time course 0hI-0hNI	1.05882	0.799
Time course 12hI-12hNI	0.94478	0.581
Time course 36hI-36hNI	0.88025	0.136
Time course 60hI-60hNI	0.30295	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)	0.82239	0.289
transgenic ySAMdc/azygous control (breaker)	2.45272	0.248
transgenic ySAMdc/azygous control (red)	1.04311	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.85943	0.064

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.68375	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.74632	0.096
Manapal/WT (break)	4.8932	0.183
Manapal/WT (red)	1.71545	0.413