Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.19.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08989	1
27DAP/17DAP	1.2822	0.761
39DAP/27DAP	1.22416	0.857
41DAP/39DAP	1.06824	0.772
42DAP/41DAP	1.00185	1
43DAP/42DAP	1.3942	0.662
47DAP/43DAP	0.84946	0.522
52DAP/47DAP	1.35458	0.559
57DAP/52DAP	1.09043	0.982

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97908	0.589
17DAP/reference	0.96121	0.503
27DAP/reference	1.03478	0.797
39DAP/reference	1.04483	0.828
41DAP/reference	0.7908	0.085
42DAP/reference	1.03876	0.608
43DAP/reference	0.99873	0.84
47DAP/reference	1.11151	0.318
52DAP/reference	1.05828	0.912
57DAP/reference	1.00675	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.34931	0.071
27DAP/17DAP	1.18685	0.932
39DAP/27DAP	0.87732	0.188
41DAP/39DAP	1.21863	0.65
42DAP/41DAP	1.27123	0.663
43DAP/42DAP	0.9092	0.522
47DAP/43DAP	1.12016	0.805
52DAP/47DAP	0.90005	0.753
57DAP/52DAP	1.40052	0.091
57DAP/7DAP	0.92561	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79886	0.071
17DAP/reference	0.85391	0.082
27DAP/reference	0.94554	0.248
39DAP/reference	0.94841	0.411
41DAP/reference	0.85236	0.153
42DAP/reference	0.72984	0.038
43DAP/reference	0.93583	0.21
47DAP/reference	0.93496	0.504
52DAP/reference	0.73303	0.035
57DAP/reference	0.77907	0.02

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85423	0.124
17DAP/reference	0.8292	0.176
27DAP/reference	0.96991	0.501
39DAP/reference	0.9066	0.257
41DAP/reference	0.95141	0.393
42DAP/reference	0.93024	0.392
43DAP/reference	0.82267	0.105
47DAP/reference	1.01715	0.833
52DAP/reference	0.93682	0.171
57DAP/reference	0.91297	0.259

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00605	1
17DAP/reference	0.85523	0.286
27DAP/reference	1.06292	0.392
39DAP/reference	0.98333	0.504
41DAP/reference	0.95498	0.459
42DAP/reference	0.8233	0.087
43DAP/reference	0.93969	0.449
47DAP/reference	0.84011	0.12
52DAP/reference	1.61294	0.631
57DAP/reference	1.08714	0.717

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07908	0.966
26DAP/20DAP	1.42691	0.453
34DAP/26DAP	1.18757	0.972
51DAP/34DAP	1.29743	0.483
52DAP/51DAP	0.7112	1
53DAP/52DAP	0.968	0.649
55DAP/53DAP	1.0544	1
57DAP/55DAP	1.00102	0.955
62DAP/57DAP	0.88147	0.681
68DAP/62DAP	0.88472	0.7
68DAP/14DAP	0.73259	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.33573	0.627

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.68216	0.044
Immature Eggplant/Mature Eggplant	0.91719	0.594
Ripe Pepper/Ripe Tomato	0.38405	0.224
Mature Eggplant/Ripe Tomato	1.04428	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.99305
12-2/M82	N/A	N/A
12-4/M82	0.68043
1-3/M82	N/A	N/A
2-1-1/M82	0.6326
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
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	0.81035
5-3/M82	0.87588
6-2/M82	N/A	N/A
6-3/M82	1.2392
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.21297	0.365
IL2-6/WTpooled	1.29115	0.659
IL7-5/WTpooled	1.04057	1
IL7-3/WTpooled	1.13738	1
IL12-4/WTpooled	1.34237	0.52
IL1-4/WTpooled	0.99173	0.834
WT/WTpooled	1.01119	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	0.98316	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.21136
DC3000/delta hrp 6h	1.43624	1
DC3000/delta hrp 12h	0.88165	1
DC3000/delta hrp 24h	0.81878	0.163

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	1.63313

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.81211	1
Exp 36h	N/A	N/A
Exp 60h	0.88345	0.29

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98319	1
Var 0h	0.62806	1
Var 12h I row2-row1	1.35839	0.506
Var 12h NI row2-row1	1.1566	1
Var 36h I row2-row1	1.07576	0.742
Var 36h NI row2-row1	0.70131	0.478
Var 60h I row2-row1	0.99511	1
Var 60h NI row2-row1	1.11957	0.904
Time course 0hI-0hNI	0.97854	0.94
Time course 12hI-12hNI	1.04936	0.747
Time course 36hI-36hNI	0.99124	0.632
Time course 60hI-60hNI	1.09697	0.187

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)	1.06861	0.384
transgenic ySAMdc/azygous control (breaker)	0.87889	0.173
transgenic ySAMdc/azygous control (red)	0.89607	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.28962	0.073

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.78588	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.78602	1
Manapal/WT (break)	0.96645	1
Manapal/WT (red)	0.74757	0.181