Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.19.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	3.2174	0.303
27DAP/17DAP	1.33346	0.769
39DAP/27DAP	0.97899	0.733
41DAP/39DAP	1.06986	1
42DAP/41DAP	1.17967	0.786
43DAP/42DAP	0.99672	0.932
47DAP/43DAP	0.8022	0.41
52DAP/47DAP	0.91289	0.742
57DAP/52DAP	1.18553	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.67374	0.033
17DAP/reference	1.58857	0.092
27DAP/reference	2.38878	0.008
39DAP/reference	2.26831	0.016
41DAP/reference	1.66329	0.038
42DAP/reference	3.17493	0.001
43DAP/reference	3.84489	0.006
47DAP/reference	4.91691	0.001
52DAP/reference	1.97432	0.01
57DAP/reference	1.94285	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03211	1
27DAP/17DAP	0.92466	0.854
39DAP/27DAP	1.24123	0.526
41DAP/39DAP	0.93526	0.781
42DAP/41DAP	1.278	0.193
43DAP/42DAP	0.97946	0.854
47DAP/43DAP	0.92857	0.617
52DAP/47DAP	1.53174	0.122
57DAP/52DAP	1.56423	0.123
57DAP/7DAP	1.55158	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80413	0.108
17DAP/reference	1.26861	0.02
27DAP/reference	1.15091	0.026
39DAP/reference	1.7654	0.006
41DAP/reference	1.934	0.01
42DAP/reference	2.49148	0.006
43DAP/reference	3.05949	0.006
47DAP/reference	3.85372	0.014
52DAP/reference	2.54236	0.007
57DAP/reference	2.73834	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.37378	0.006
17DAP/reference	2.07944	0.008
27DAP/reference	3.04658	0.012
39DAP/reference	2.72447	0.011
41DAP/reference	3.58482	0.005
42DAP/reference	3.19815	0.007
43DAP/reference	1.49359	0.605
47DAP/reference	2.3929	0.008
52DAP/reference	2.2204	0.006
57DAP/reference	1.18231	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.37924	0.032
17DAP/reference	0.93253	0.452
27DAP/reference	0.94688	0.376
39DAP/reference	1.37509	0.015
41DAP/reference	0.9457	0.417
42DAP/reference	1.60667	0.08
43DAP/reference	2.90542	0.051
47DAP/reference	3.8385	0.005
52DAP/reference	2.32512	0.033
57DAP/reference	5.47603	0.014

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10013	0.966
26DAP/20DAP	2.24787	0.654
34DAP/26DAP	1.89943	0.819
51DAP/34DAP	1.47899	0.706
52DAP/51DAP	3.19971	0.051
53DAP/52DAP	1.05604	0.935
55DAP/53DAP	1.41163	0.103
57DAP/55DAP	0.63038	0.035
62DAP/57DAP	0.8999	0.681
68DAP/62DAP	1.12771	0.8
68DAP/14DAP	0.81519	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.551	0.038

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.16792	0.075
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	0.82262	0.125
Ripe Pepper/Ripe Tomato	0.22335	0.224
Mature Eggplant/Ripe Tomato	0.13326	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9345	0.944
1-1-2/M82	1.17708	1
12-2/M82	0.95616	0.955
12-4/M82	0.98703
1-3/M82	1.21126	1
2-1-1/M82	0.84913	0.465
2-1/M82	0.89906	0.74
2-6/M82	0.95244	1
3-2/M82	1.14347
4-1-1/M82	0.91807	1
4-1/M82	0.87305
4-3-2/M82	0.62709
4-3/M82	0.91376	0.72
5-3/M82	1.0174	1
6-2/M82	0.9457	1
6-3/M82	0.99944	1
7-1/M82	0.88789	1
7-2/M82	0.9317	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.10408	0.493
IL2-6/WTpooled	0.85646	1
IL7-5/WTpooled	1.04045	1
IL7-3/WTpooled	1.18052	1
IL12-4/WTpooled	1.27783	0.673
IL1-4/WTpooled	0.89565	0.699
WT/WTpooled	1.03287	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	0.99217	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0204	1
DC3000/delta hrp 6h	0.90199	0.95
DC3000/delta hrp 12h	0.98067	1
DC3000/delta hrp 24h	0.8057	0.076

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.13519
DC3000 delta B/DC3000 delta AB	1.06528	0.55

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07285	1
Exp 36h	1.15342	0.693
Exp 60h	1.07698	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9299	1
Var 0h	1.18579	0.98
Var 12h I row2-row1	0.79745	0.418
Var 12h NI row2-row1	0.90073	0.713
Var 36h I row2-row1	0.8875	0.805
Var 36h NI row2-row1	1.02443	1
Var 60h I row2-row1	0.97535
Var 60h NI row2-row1	0.68745	0.977
Time course 0hI-0hNI	0.99159	1
Time course 12hI-12hNI	0.9545	0.506
Time course 36hI-36hNI	0.88371	0.166
Time course 60hI-60hNI	0.67228	0.006

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)	1.03694	0.863
transgenic ySAMdc/azygous control (breaker)	0.65211	0.15
transgenic ySAMdc/azygous control (red)	0.82364	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.17712	0.047

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.82898	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.99793	1
Manapal/WT (break)	0.96061	1
Manapal/WT (red)	1.2892	0.413