Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.10.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0141	0.683
27DAP/17DAP	1.60801	0.646
39DAP/27DAP	1.63677	0.12
41DAP/39DAP	0.89213	0.558
42DAP/41DAP	0.94827	1
43DAP/42DAP	1.01494	0.918
47DAP/43DAP	0.91293	0.652
52DAP/47DAP	1.66199	0.226
57DAP/52DAP	1.63263	0.894

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01223	0.526
17DAP/reference	0.6142	0.018
27DAP/reference	0.77284	0.157
39DAP/reference	0.70542	0.106
41DAP/reference	0.57901	0.031
42DAP/reference	2.11836	0.001
43DAP/reference	1.23248	0.04
47DAP/reference	1.20859	0.254
52DAP/reference	0.71644	0.108
57DAP/reference	1.01295	0.805

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.72235	0.033
27DAP/17DAP	0.68207	0.097
39DAP/27DAP	1.88064	0.047
41DAP/39DAP	2.22474	0.014
42DAP/41DAP	0.49987	0.011
43DAP/42DAP	1.52273	0.015
47DAP/43DAP	1.04878	0.897
52DAP/47DAP	2.1808	0.048
57DAP/52DAP	2.35013	0.029
57DAP/7DAP	1.82079	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23369	0.205
17DAP/reference	1.05355	0.477
27DAP/reference	1.51027	0.018
39DAP/reference	1.54916	0.013
41DAP/reference	1.52505	0.018
42DAP/reference	2.47409	0.006
43DAP/reference	2.66084	0.006
47DAP/reference	2.19218	0.014
52DAP/reference	1.98423	0.017
57DAP/reference	2.50105	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.61662	0.032
17DAP/reference	0.78202	0.016
27DAP/reference	1.08087	0.67
39DAP/reference	0.82046	0.085
41DAP/reference	1.18895	0.094
42DAP/reference	1.27105	0.018
43DAP/reference	1.20981	0.761
47DAP/reference	2.3562	0.009
52DAP/reference	0.54267	0.004
57DAP/reference	1.20649	0.755

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98368	0.607
17DAP/reference	0.77936	0.154
27DAP/reference	1.3346	0.025
39DAP/reference	1.19619	0.318
41DAP/reference	0.88476	0.058
42DAP/reference	1.04736	0.818
43DAP/reference	1.28092	0.085
47DAP/reference	1.12283	0.966
52DAP/reference	1.62554	0.032
57DAP/reference	1.9387	0.014

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0785	1
26DAP/20DAP	1.00043	1
34DAP/26DAP	1.37516	1
51DAP/34DAP	0.78113	0.268
52DAP/51DAP	0.62001
53DAP/52DAP	1.29162	0.688
55DAP/53DAP	2.08068	0.629
57DAP/55DAP	0.91138	0.647
62DAP/57DAP	0.69803	0.088
68DAP/62DAP	2.17165	0.285
68DAP/14DAP	1.33552	0.694

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	17.6224	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.1532	0.024
Immature Eggplant/Mature Eggplant	9.81376	0.049
Ripe Pepper/Ripe Tomato	0.07737	0.224
Mature Eggplant/Ripe Tomato	0.10848	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96797	0.944
1-1-2/M82	1.10346	1
12-2/M82	1.58385	1
12-4/M82	1.09574	0.611
1-3/M82	4.68789	0.248
2-1-1/M82	1.77503	0.439
2-1/M82	1.37108
2-6/M82	1.7698	0.425
3-2/M82	1.66833	0.549
4-1-1/M82	2.88204	0.968
4-1/M82	1.29997	0.466
4-3-2/M82	2.45527	0.246
4-3/M82	1.68677	0.268
5-3/M82	0.84138	0.642
6-2/M82	3.6385	1
6-3/M82	0.41371	0.857
7-1/M82	0.97024
7-2/M82	2.59727	0.324
9-3-2/M82	1.41877	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.01426	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.0321	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.97698	0.402
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	1.11581	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.14073	0.629
DC3000/delta hrp 6h	1.34475	0.672
DC3000/delta hrp 12h	1.04712	1
DC3000/delta hrp 24h	2.41962	0.025

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.15044	0.053
DC3000 delta B/DC3000 delta AB	2.93878	0.081

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.24327	0.254
Exp 36h	2.53608	0.489
Exp 60h	1.5304	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05842	1
Var 0h	0.90966	1
Var 12h I row2-row1	1.08167	0.544
Var 12h NI row2-row1	1.11064	0.649
Var 36h I row2-row1	1.0822	0.908
Var 36h NI row2-row1	1.00517	1
Var 60h I row2-row1	1.01903	1
Var 60h NI row2-row1	0.88219	0.69
Time course 0hI-0hNI	1.12213	0.451
Time course 12hI-12hNI	2.78189	0.004
Time course 36hI-36hNI	4.26798	0.004
Time course 60hI-60hNI	4.16842	0.008

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)	1.01562	0.862
transgenic ySAMdc/azygous control (breaker)	0.6237	0.137
transgenic ySAMdc/azygous control (red)	1.14115	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	2.09288	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.82716	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.68061	0.172
Manapal/WT (break)	0.76678	1
Manapal/WT (red)	0.96425	0.728