Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.2.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05442	0.927
27DAP/17DAP	0.86321	0.63
39DAP/27DAP	1.44859	0.26
41DAP/39DAP	0.96536	0.715
42DAP/41DAP	0.8537	1
43DAP/42DAP	1.17937	0.867
47DAP/43DAP	0.56921	0.074
52DAP/47DAP	1.39187	0.718
57DAP/52DAP	0.76135	0.759

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.46832	0.016
17DAP/reference	0.71846	0.038
27DAP/reference	0.54262	0.018
39DAP/reference	0.43836	0.013
41DAP/reference	0.51862	0.016
42DAP/reference	1.56216	0.001
43DAP/reference	0.8344	0.029
47DAP/reference	0.5574	0.01
52DAP/reference	0.66062	0.065
57DAP/reference	0.9973	0.736

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.34945	0.044
27DAP/17DAP	0.80664	0.169
39DAP/27DAP	0.74414	0.064
41DAP/39DAP	1.08431	0.807
42DAP/41DAP	0.81177	0.098
43DAP/42DAP	1.49392	0.016
47DAP/43DAP	1.09549	0.699
52DAP/47DAP	0.69466	0.101
57DAP/52DAP	1.02977	1
57DAP/7DAP	1.0741

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	4.04235	0.024
17DAP/reference	1.0118	1
27DAP/reference	2.09863	0.009
39DAP/reference	1.59348	0.01
41DAP/reference	2.64862	0.009
42DAP/reference	2.84862	0.006
43DAP/reference	5.03625	0.006
47DAP/reference	2.67328	0.014
52DAP/reference	2.38777	0.007
57DAP/reference	1.0936	0.571

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.15613	0.053
17DAP/reference	1.05441	0.805
27DAP/reference	1.5513	0.075
39DAP/reference	2.42554	0.011
41DAP/reference	2.67509	0.005
42DAP/reference	1.96863	0.011
43DAP/reference	0.77702	0.144
47DAP/reference	0.98448	0.5
52DAP/reference	0.71501	0.007
57DAP/reference	0.48254	0.01

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.86398	0.016
17DAP/reference	0.90406	0.407
27DAP/reference	1.31858	0.105
39DAP/reference	1.40847	0.041
41DAP/reference	0.93701	0.148
42DAP/reference	1.45589	0.036
43DAP/reference	1.86528	0.094
47DAP/reference	0.53227	0.005
52DAP/reference	0.93118	0.529
57DAP/reference	0.91434	0.333

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.56592
26DAP/20DAP	1.43886	0.204
34DAP/26DAP	1.04244	1
51DAP/34DAP	0.76972	0.074
52DAP/51DAP	0.81911	1
53DAP/52DAP	1.10953	0.797
55DAP/53DAP	0.95503	0.632
57DAP/55DAP	0.99641	0.819
62DAP/57DAP	0.18214	0.003
68DAP/62DAP	0.88665	0.052
68DAP/14DAP	0.99044

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.17508	0.212

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.30874	0.577
Immature Eggplant/Mature Eggplant	2.1593	0.05
Ripe Pepper/Ripe Tomato	0.04643	1
Mature Eggplant/Ripe Tomato	0.06998	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.75815
1-1-2/M82	1.07368
12-2/M82	N/A	N/A
12-4/M82	0.92397
1-3/M82	N/A	N/A
2-1-1/M82	1.45946
2-1/M82	N/A	N/A
2-6/M82	1.30607	0.425
3-2/M82	1.39338
4-1-1/M82	N/A	N/A
4-1/M82	0.96175
4-3-2/M82	N/A	N/A
4-3/M82	0.47991	0.578
5-3/M82	1.04344	1
6-2/M82	3.98879
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	2.43974	0.324
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.07631	0.365
IL2-6/WTpooled	0.3182
IL7-5/WTpooled	0.91086	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.89754	0.516
IL1-4/WTpooled	1.08672	1
WT/WTpooled	N/A	N/A

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	0.79287	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.85448	0.868
DC3000/delta hrp 6h	1.00526	1
DC3000/delta hrp 12h	1.07816
DC3000/delta hrp 24h	0.7116	0.059

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.03924	0.648
DC3000 delta B/DC3000 delta AB	0.90236	0.27

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.61857	1
Exp 36h	N/A	N/A
Exp 60h	2.30183	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	0.93706	1
Var 0h	1.07746	1
Var 12h I row2-row1	0.7904	0.467
Var 12h NI row2-row1	0.97787	0.906
Var 36h I row2-row1	1.22626	0.41
Var 36h NI row2-row1	1.13176	1
Var 60h I row2-row1	1.11297	1
Var 60h NI row2-row1	1.00973	1
Time course 0hI-0hNI	1.02278	1
Time course 12hI-12hNI	0.85966	0.163
Time course 36hI-36hNI	0.81115	0.023
Time course 60hI-60hNI	0.17971	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)	1.8605	0.289
transgenic ySAMdc/azygous control (breaker)	0.63858	0.15
transgenic ySAMdc/azygous control (red)	0.79045	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9129	0.071

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.57334	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.34023	1
Manapal/WT (break)	0.78745	1
Manapal/WT (red)	0.76384	0.424