Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.14.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09546	0.709
27DAP/17DAP	0.89471	0.766
39DAP/27DAP	0.83656	0.402
41DAP/39DAP	1.08033	0.715
42DAP/41DAP	0.96573	1
43DAP/42DAP	0.86788	0.665
47DAP/43DAP	1.04678	0.966
52DAP/47DAP	1.12914	0.837
57DAP/52DAP	0.98915	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86006	0.089
17DAP/reference	0.77404	0.009
27DAP/reference	0.78564	0.015
39DAP/reference	0.73032	0.023
41DAP/reference	0.76268	0.013
42DAP/reference	0.85494	0.003
43DAP/reference	0.78636	0.014
47DAP/reference	0.78731	0.001
52DAP/reference	0.79035	0.048
57DAP/reference	0.70719	0.01

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09814	0.135
27DAP/17DAP	0.92757	0.363
39DAP/27DAP	0.94386	0.456
41DAP/39DAP	1.03744	0.837
42DAP/41DAP	0.97258	0.726
43DAP/42DAP	0.94443	0.415
47DAP/43DAP	0.98234	0.911
52DAP/47DAP	1.05441	0.823
57DAP/52DAP	1.01068	1
57DAP/7DAP	1.02365	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94872	0.246
17DAP/reference	0.99478	0.693
27DAP/reference	0.92428	0.012
39DAP/reference	0.9468	0.021
41DAP/reference	0.76515	0.194
42DAP/reference	1.01353
43DAP/reference	0.97125	0.385
47DAP/reference	0.61173	0.05
52DAP/reference	0.90971	0.017
57DAP/reference	0.85552	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80468	0.031
17DAP/reference	0.83913	0.007
27DAP/reference	0.94433	0.352
39DAP/reference	0.76711	0.081
41DAP/reference	1.00464	0.683
42DAP/reference	0.94557	0.321
43DAP/reference	0.69871	0.022
47DAP/reference	0.84671	0.031
52DAP/reference	0.70395	0.003
57DAP/reference	0.68705	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17481	0.041
17DAP/reference	1.24407	0.163
27DAP/reference	1.10874	0.425
39DAP/reference	0.98668	0.693
41DAP/reference	0.91993	0.209
42DAP/reference	0.91843	0.071
43DAP/reference	0.83117	0.216
47DAP/reference	0.67948	0.006
52DAP/reference	0.76474	0.123
57DAP/reference	0.8181	0.045

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95194	1
26DAP/20DAP	1.04414	0.875
34DAP/26DAP	0.88051	0.098
51DAP/34DAP	0.90389	0.252
52DAP/51DAP	0.97448	1
53DAP/52DAP	0.9777	0.868
55DAP/53DAP	1.04443	0.898
57DAP/55DAP	0.86133	0.521
62DAP/57DAP	1.06958	0.35
68DAP/62DAP	0.90186	0.641
68DAP/14DAP	1.00037	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.94132	0.399

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.50345	0.058
Mature Green Tomato/Ripe Tomato	1.65488	0.02
Immature Eggplant/Mature Eggplant	0.41895	0.057
Ripe Pepper/Ripe Tomato	2.48053	1
Mature Eggplant/Ripe Tomato	25.8715	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.07241	0.574
1-1-2/M82	0.81602	1
12-2/M82	0.99951	1
12-4/M82	1.01886	1
1-3/M82	0.89641	0.378
2-1-1/M82	0.95661
2-1/M82	N/A	N/A
2-6/M82	0.98626	1
3-2/M82	1.17615
4-1-1/M82	N/A	N/A
4-1/M82	0.7023	1
4-3-2/M82	0.80414	0.487
4-3/M82	0.86165
5-3/M82	1.02627	1
6-2/M82	1.12562
6-3/M82	0.95654	1
7-1/M82	N/A	N/A
7-2/M82	0.97191	1
9-3-2/M82	0.8937

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.95455	1
IL2-6/WTpooled	1.04165	0.531
IL7-5/WTpooled	0.97578	1
IL7-3/WTpooled	1.1013	1
IL12-4/WTpooled	0.92997	0.566
IL1-4/WTpooled	0.98333	1
WT/WTpooled	0.96712	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	1.15468	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99644	1
DC3000/delta hrp 6h	1.04839	1
DC3000/delta hrp 12h	0.93792	1
DC3000/delta hrp 24h	0.93993	0.682

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.64759	0.106

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00828	1
Exp 36h	0.85261	0.661
Exp 60h	0.854	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03307	1
Var 0h	0.9229	1
Var 12h I row2-row1	1.06425	0.506
Var 12h NI row2-row1	0.95331	0.906
Var 36h I row2-row1	0.90004	1
Var 36h NI row2-row1	1.01906	1
Var 60h I row2-row1	1.75687	0.562
Var 60h NI row2-row1	1.10353	0.904
Time course 0hI-0hNI	1.02334	1
Time course 12hI-12hNI	1.05671	0.77
Time course 36hI-36hNI	1.02996	0.722
Time course 60hI-60hNI	0.36077	0.007

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)	0.90585	0.567
transgenic ySAMdc/azygous control (breaker)	4.43409	0.165
transgenic ySAMdc/azygous control (red)	1.24786	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.75827	0.077

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.35785	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	39.1023	0.084
Manapal/WT (break)	9.60428	0.123
Manapal/WT (red)	2.5666	1