Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.12.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.36934	0.523
27DAP/17DAP	1.17935	0.868
39DAP/27DAP	1.25221	0.796
41DAP/39DAP	0.91104	0.632
42DAP/41DAP	1.15419	0.929
43DAP/42DAP	0.95689	0.851
47DAP/43DAP	1.11878	0.889
52DAP/47DAP	1.25629	0.709
57DAP/52DAP	1.00074	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31807	0.008
17DAP/reference	1.1565	0.08
27DAP/reference	1.27135	0.132
39DAP/reference	1.45724	0.029
41DAP/reference	1.53196	0.015
42DAP/reference	1.20466	0.001
43DAP/reference	0.97922	0.675
47DAP/reference	1.19725	0.148
52DAP/reference	1.2012	0.026
57DAP/reference	1.2411	0.463

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91977	0.311
27DAP/17DAP	1.07209	0.932
39DAP/27DAP	1.04704	0.672
41DAP/39DAP	1.09958	0.799
42DAP/41DAP	0.9597	0.708
43DAP/42DAP	1.07187	0.382
47DAP/43DAP	1.04373	0.914
52DAP/47DAP	0.98416	0.917
57DAP/52DAP	1.08703	0.67
57DAP/7DAP	0.98393	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95389	0.495
17DAP/reference	1.11521	0.437
27DAP/reference	0.9589	0.303
39DAP/reference	0.87988	0.109
41DAP/reference	0.81187	0.052
42DAP/reference	0.83611	0.04
43DAP/reference	0.94782	0.292
47DAP/reference	0.94644	0.504
52DAP/reference	0.92719	0.232
57DAP/reference	0.93861	0.314

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.60163	0.052
17DAP/reference	1.71111	0.007
27DAP/reference	1.6215	0.028
39DAP/reference	1.31504	0.141
41DAP/reference	1.33661	0.018
42DAP/reference	1.61236	0.008
43DAP/reference	1.85029	0.076
47DAP/reference	1.7865	0.008
52DAP/reference	1.54628	0.012
57DAP/reference	1.57553	0.033

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09069	0.28
17DAP/reference	1.27324	0.273
27DAP/reference	1.09432	0.392
39DAP/reference	0.97093	0.504
41DAP/reference	1.15524	0.84
42DAP/reference	1.17452	0.138
43DAP/reference	1.23893	0.474
47DAP/reference	1.17952	0.61
52DAP/reference	1.00109	0.908
57DAP/reference	1.3758	0.147

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01281	1
26DAP/20DAP	1.01358	1
34DAP/26DAP	0.9183	0.777
51DAP/34DAP	1.34082	0.058
52DAP/51DAP	0.96793	1
53DAP/52DAP	0.901	0.621
55DAP/53DAP	0.99346	0.894
57DAP/55DAP	1.41042	0.407
62DAP/57DAP	0.77481	0.088
68DAP/62DAP	1.24027	0.253
68DAP/14DAP	0.70922	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.65286	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.19037	0.055
Mature Green Tomato/Ripe Tomato	1.15755	0.437
Immature Eggplant/Mature Eggplant	0.46242	0.057
Ripe Pepper/Ripe Tomato	22.774	0.256
Mature Eggplant/Ripe Tomato	N/A	N/A

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	0.90616
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	1.03161	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.72407
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.88814	1
IL12-4/WTpooled	0.60833	0.543
IL1-4/WTpooled	1.2912
WT/WTpooled	1.18271	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	0.84922	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9911	1
DC3000/delta hrp 6h	1.22069	1
DC3000/delta hrp 12h	1.10897	1
DC3000/delta hrp 24h	1.08709	0.673

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.95436	0.803
DC3000 delta B/DC3000 delta AB	1.21351	0.412

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.63967	0.265
Exp 36h	0.76214	0.749
Exp 60h	0.61793	0.251

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99173	1
Var 0h	1.01921	0.98
Var 12h I row2-row1	0.91183	0.418
Var 12h NI row2-row1	0.93842	0.546
Var 36h I row2-row1	0.93843	1
Var 36h NI row2-row1	0.85944	0.61
Var 60h I row2-row1	0.92666	0.306
Var 60h NI row2-row1	0.95876	0.866
Time course 0hI-0hNI	0.99711	1
Time course 12hI-12hNI	0.99566	1
Time course 36hI-36hNI	1.0182	0.881
Time course 60hI-60hNI	1.26527	0.033

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)	0.94994	0.529
transgenic ySAMdc/azygous control (breaker)	1.09198	1
transgenic ySAMdc/azygous control (red)	1.3409	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94623	0.087

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.88979	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.90649	0.083
Manapal/WT (break)	1.70023	1
Manapal/WT (red)	1.33465	1