Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.11.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92398	0.586
27DAP/17DAP	0.9629	0.947
39DAP/27DAP	0.77305	0.397
41DAP/39DAP	1.35188	0.222
42DAP/41DAP	1.20053	0.868
43DAP/42DAP	0.82982	0.7
47DAP/43DAP	1.16848	0.746
52DAP/47DAP	1.6353	0.305
57DAP/52DAP	0.93888	0.936

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91468	0.182
17DAP/reference	0.98637	0.701
27DAP/reference	0.98783	0.711
39DAP/reference	0.95438	0.5
41DAP/reference	0.98204	0.814
42DAP/reference	0.86628	0.015
43DAP/reference	1.02716	0.678
47DAP/reference	0.83836	0.002
52DAP/reference	0.84752	0.108
57DAP/reference	0.81521	0.022

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85807	0.251
27DAP/17DAP	1.06396	0.867
39DAP/27DAP	1.207	0.436
41DAP/39DAP	1.08114	0.876
42DAP/41DAP	1.13565	0.55
43DAP/42DAP	0.99585	0.96
47DAP/43DAP	1.03374	0.957
52DAP/47DAP	0.99853	0.97
57DAP/52DAP	1.0493	0.783
57DAP/7DAP	1.23834	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8794	0.058
17DAP/reference	0.87793	0.012
27DAP/reference	0.91728	0.02
39DAP/reference	0.87289	0.011
41DAP/reference	0.83319	0.024
42DAP/reference	0.80046	0.01
43DAP/reference	0.85191	0.031
47DAP/reference	0.82572	0.128
52DAP/reference	0.81436	0.083
57DAP/reference	0.78874	0.015

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03246	0.776
17DAP/reference	0.94959	0.297
27DAP/reference	0.83231	0.104
39DAP/reference	0.83431	0.122
41DAP/reference	0.84681	0.083
42DAP/reference	0.82903	0.081
43DAP/reference	1.04025	0.802
47DAP/reference	0.88185	0.046
52DAP/reference	0.95309	0.22
57DAP/reference	1.21161	0.182

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94623	0.29
17DAP/reference	0.99022	0.751
27DAP/reference	0.85689	0.033
39DAP/reference	0.92197	0.163
41DAP/reference	0.88025	0.064
42DAP/reference	0.87789	0.287
43DAP/reference	0.77027	0.125
47DAP/reference	1.00703	0.687
52DAP/reference	0.94214	0.472
57DAP/reference	0.53248	0.018

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06558	0.916
26DAP/20DAP	0.90218	0.512
34DAP/26DAP	1.03977	1
51DAP/34DAP	0.89892	0.376
52DAP/51DAP	0.98995	1
53DAP/52DAP	1.11808	0.797
55DAP/53DAP	1.01368	1
57DAP/55DAP	1.08008	0.906
62DAP/57DAP	1.09991	0.8
68DAP/62DAP	0.91629	0.722
68DAP/14DAP	0.89452	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.81581	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	0.78676	0.119
Immature Eggplant/Mature Eggplant	1.51363	0.311
Ripe Pepper/Ripe Tomato	0.91995
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92284	0.944
1-1-2/M82	0.78563	0.958
12-2/M82	1.14139	1
12-4/M82	0.9465	1
1-3/M82	0.89405	0.441
2-1-1/M82	1.17809	0.422
2-1/M82	1.24015	0.312
2-6/M82	1.03308	0.425
3-2/M82	0.94641	1
4-1-1/M82	0.98447	1
4-1/M82	0.83368	1
4-3-2/M82	0.89832	0.698
4-3/M82	1.01207	1
5-3/M82	0.95567	1
6-2/M82	0.92379	1
6-3/M82	1.00969	1
7-1/M82	0.89922	0.803
7-2/M82	1.05482	1
9-3-2/M82	0.97294

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.97133	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.91816	0.294
IL12-4/WTpooled	0.98601	1
IL1-4/WTpooled	0.93064
WT/WTpooled	1.0452	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	0.86985

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01612	1
DC3000/delta hrp 6h	0.95535
DC3000/delta hrp 12h	0.60047	1
DC3000/delta hrp 24h	0.83398	0.126

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.49072
DC3000 delta B/DC3000 delta AB	1.08743	0.42

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	1.42109	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02241	1
Var 0h	0.53994	0.98
Var 12h I row2-row1	1.1527	0.222
Var 12h NI row2-row1	0.9906	1
Var 36h I row2-row1	0.98766	1
Var 36h NI row2-row1	0.87889	0.61
Var 60h I row2-row1	1.89688	1
Var 60h NI row2-row1	1.29709	0.904
Time course 0hI-0hNI	1.05083	0.799
Time course 12hI-12hNI	0.98872	0.956
Time course 36hI-36hNI	0.94972	0.269
Time course 60hI-60hNI	1.27418	0.015

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)	0.95977	0.428
transgenic ySAMdc/azygous control (breaker)	1.26446	0.248
transgenic ySAMdc/azygous control (red)	0.95554	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02058	0.35

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.14243	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.45212	0.307
Manapal/WT (break)	1.15664	1
Manapal/WT (red)	1.23456	0.164