Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.4.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.59007	0.03
27DAP/17DAP	0.47509	0.029
39DAP/27DAP	0.89757	0.608
41DAP/39DAP	0.51699	0.047
42DAP/41DAP	0.73321	0.774
43DAP/42DAP	1.29484	0.527
47DAP/43DAP	0.55592	0.08
52DAP/47DAP	0.94873	0.772
57DAP/52DAP	1.1495	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.57221	0.01
17DAP/reference	1.03996	0.874
27DAP/reference	1.03891	1
39DAP/reference	0.77893	0.146
41DAP/reference	0.58318	0.016
42DAP/reference	0.95307	0.268
43DAP/reference	0.73028	0.088
47DAP/reference	0.50804	0.001
52DAP/reference	0.43952	0.013
57DAP/reference	0.76555	0.022

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.73802	0.141
27DAP/17DAP	1.00781	1
39DAP/27DAP	0.67922	0.032
41DAP/39DAP	0.59612	0.031
42DAP/41DAP	0.98449	0.776
43DAP/42DAP	1.07188	0.664
47DAP/43DAP	0.96515	0.886
52DAP/47DAP	1.01281	0.947
57DAP/52DAP	1.13491	0.662
57DAP/7DAP	0.39148	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15503	0.325
17DAP/reference	0.77265	0.049
27DAP/reference	0.58549	0.01
39DAP/reference	0.73695	0.011
41DAP/reference	0.54348	0.011
42DAP/reference	0.55792	0.013
43DAP/reference	0.47346	0.015
47DAP/reference	0.51266	0.026
52DAP/reference	0.56916	0.013
57DAP/reference	0.49866	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78421	0.093
17DAP/reference	1.25389	0.92
27DAP/reference	0.72448	0.087
39DAP/reference	0.61059	0.015
41DAP/reference	0.88027	0.04
42DAP/reference	0.86604	0.108
43DAP/reference	0.5898	0.035
47DAP/reference	1.06789	0.867
52DAP/reference	0.40957	0.003
57DAP/reference	0.37373	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	4.15406	0.032
17DAP/reference	1.63733	0.117
27DAP/reference	1.15934	0.216
39DAP/reference	0.93021	0.328
41DAP/reference	0.8045	0.086
42DAP/reference	5.97467	0.027
43DAP/reference	4.77983	0.057
47DAP/reference	0.43139	0.004
52DAP/reference	5.57999	0.278
57DAP/reference	2.02436	0.867

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00236	1
26DAP/20DAP	0.97042	1
34DAP/26DAP	0.87544	0.61
51DAP/34DAP	0.98281	0.873
52DAP/51DAP	1.00126	1
53DAP/52DAP	0.92266	0.64
55DAP/53DAP	0.72611	0.293
57DAP/55DAP	1.15163	0.643
62DAP/57DAP	1.16906	1
68DAP/62DAP	1.26598	0.944
68DAP/14DAP	0.62485	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.7282	0.115

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.03571	0.058
Mature Green Tomato/Ripe Tomato	24.6689	0.015
Immature Eggplant/Mature Eggplant	0.4687	0.062
Ripe Pepper/Ripe Tomato	20.539	1
Mature Eggplant/Ripe Tomato	11.443	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.91383
1-1-2/M82	0.8471
12-2/M82	N/A	N/A
12-4/M82	0.5885
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	1.28905
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	1.06104
5-3/M82	0.97436	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	1.30595
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.9644	1
IL2-6/WTpooled	1.22913	0.427
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.1072	1
IL12-4/WTpooled	0.95065	0.71
IL1-4/WTpooled	1.08237	0.426
WT/WTpooled	0.92777	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	0.90147	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97072	1
DC3000/delta hrp 6h	0.94052	0.95
DC3000/delta hrp 12h	1.16925	1
DC3000/delta hrp 24h	0.93727	0.585

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.57047	0.028
DC3000 delta B/DC3000 delta AB	0.52455	0.023

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97178	1
Exp 36h	0.7691	0.456
Exp 60h	0.7556	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.78287	0.314
transgenic ySAMdc/azygous control (breaker)	2.9347	0.248
transgenic ySAMdc/azygous control (red)	1.31512	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.61892	0.075

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.90954	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.44574	0.14
Manapal/WT (break)	5.03316	0.13
Manapal/WT (red)	2.97392	0.222