Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.14.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.29672	0.394
27DAP/17DAP	1.2602	0.845
39DAP/27DAP	1.48477	0.38
41DAP/39DAP	1.12002	0.788
42DAP/41DAP	0.99341	1
43DAP/42DAP	0.86213	0.801
47DAP/43DAP	0.77606	0.36
52DAP/47DAP	1.73923	0.346
57DAP/52DAP	0.85961	0.81

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81646	0.052
17DAP/reference	0.87704	0.074
27DAP/reference	0.93928	0.428
39DAP/reference	0.81903	0.053
41DAP/reference	0.69302	0.014
42DAP/reference	1.09513	0.08
43DAP/reference	0.9695	0.653
47DAP/reference	1.00098	0.636
52DAP/reference	1.07138	0.8
57DAP/reference	1.13062	0.091

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.39466	0.05
27DAP/17DAP	0.79273	0.312
39DAP/27DAP	1.24282	0.347
41DAP/39DAP	0.98152	0.973
42DAP/41DAP	1.16581	0.47
43DAP/42DAP	1.30504	0.018
47DAP/43DAP	1.00276	0.99
52DAP/47DAP	1.14711	0.851
57DAP/52DAP	1.25202	0.298
57DAP/7DAP	0.86417	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18469	0.085
17DAP/reference	0.88002	0.144
27DAP/reference	0.98358	0.571
39DAP/reference	0.90368	0.198
41DAP/reference	1.00331	0.646
42DAP/reference	1.39869	0.03
43DAP/reference	1.31679	0.043
47DAP/reference	1.23015	0.124
52DAP/reference	0.88804	0.213
57DAP/reference	0.96792	0.382

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83224	0.17
17DAP/reference	0.8186	0.02
27DAP/reference	0.86601	0.144
39DAP/reference	0.9334	0.227
41DAP/reference	1.05683	0.735
42DAP/reference	0.97399	0.534
43DAP/reference	0.84766	0.075
47DAP/reference	1.0214	1
52DAP/reference	0.81481	0.072
57DAP/reference	0.61764	0.099

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81757	0.057
17DAP/reference	0.86388	0.198
27DAP/reference	1.11584	0.075
39DAP/reference	0.96724	0.43
41DAP/reference	1.0084	0.826
42DAP/reference	0.96215	0.552
43DAP/reference	0.92749	0.384
47DAP/reference	0.9305	0.306
52DAP/reference	1.07083	0.759
57DAP/reference	1.03614	0.878

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9762	1
26DAP/20DAP	0.94263	1
34DAP/26DAP	1.18462	1
51DAP/34DAP	1.34267	0.154
52DAP/51DAP	0.90039	1
53DAP/52DAP	1.15248	0.662
55DAP/53DAP	0.68287	0.13
57DAP/55DAP	1.01905	0.97
62DAP/57DAP	0.81705	0.466
68DAP/62DAP	1.31077	0.919
68DAP/14DAP	0.91229	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	4.38401	0.016

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.78037	0.058
Mature Green Tomato/Ripe Tomato	0.42706	0.086
Immature Eggplant/Mature Eggplant	9.62091	0.042
Ripe Pepper/Ripe Tomato	0.21403	0.224
Mature Eggplant/Ripe Tomato	0.13774	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99708	1
1-1-2/M82	N/A	N/A
12-2/M82	1.3139
12-4/M82	0.80405	0.358
1-3/M82	2.86444
2-1-1/M82	0.94395	1
2-1/M82	N/A	N/A
2-6/M82	1.0398	1
3-2/M82	1.19005
4-1-1/M82	N/A	N/A
4-1/M82	1.23411	1
4-3-2/M82	N/A	N/A
4-3/M82	0.98576	1
5-3/M82	1.29309	1
6-2/M82	2.32236
6-3/M82	0.72377
7-1/M82	1.43599
7-2/M82	1.67849	0.385
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.0596	1
IL2-6/WTpooled	0.92282	1
IL7-5/WTpooled	1.31767	1
IL7-3/WTpooled	0.82692	0.294
IL12-4/WTpooled	0.94307	0.71
IL1-4/WTpooled	1.51147	1
WT/WTpooled	0.94	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	1.14299	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.73529	0.063
DC3000/delta hrp 6h	1.01748	0.95
DC3000/delta hrp 12h	0.89598	1
DC3000/delta hrp 24h	1.02122	0.728

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.6876	0.25
DC3000 delta B/DC3000 delta AB	1.08993	0.472

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96056	1
Exp 36h	1.1547	1
Exp 60h	1.02791	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9586	1
Var 0h	0.93534	1
Var 12h I row2-row1	0.97202	0.856
Var 12h NI row2-row1	1.16415	0.34
Var 36h I row2-row1	1.16346	0.908
Var 36h NI row2-row1	1.19988	1
Var 60h I row2-row1	0.92412	0.952
Var 60h NI row2-row1	1.00633	1
Time course 0hI-0hNI	1.00436	1
Time course 12hI-12hNI	0.95027	0.6
Time course 36hI-36hNI	0.93619	0.38
Time course 60hI-60hNI	0.63383	0.006

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)	1.02601	1
transgenic ySAMdc/azygous control (breaker)	0.53321	0.173
transgenic ySAMdc/azygous control (red)	1.17273	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06761	0.163

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.9377	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.70254	1
Manapal/WT (break)	0.95385	1
Manapal/WT (red)	0.68767	0.181