Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.17.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94546	0.671
27DAP/17DAP	1.16749	0.849
39DAP/27DAP	0.83898	0.564
41DAP/39DAP	1.04981	0.833
42DAP/41DAP	1.02455	1
43DAP/42DAP	1.14505	0.864
47DAP/43DAP	1.24892	0.49
52DAP/47DAP	0.97849	0.72
57DAP/52DAP	0.93536	0.918

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32904	0.013
17DAP/reference	1.33455	0.013
27DAP/reference	1.26483	0.056
39DAP/reference	1.24852	0.076
41DAP/reference	1.60737	0.018
42DAP/reference	1.38889	0.001
43DAP/reference	1.10782	0.569
47DAP/reference	1.30108	0.001
52DAP/reference	1.50295	0.008
57DAP/reference	1.16222	0.419

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.784	0.103
27DAP/17DAP	1.01124	1
39DAP/27DAP	1.19023	0.429
41DAP/39DAP	0.91127	0.804
42DAP/41DAP	1.03947	0.947
43DAP/42DAP	0.91461	0.447
47DAP/43DAP	0.90542	0.554
52DAP/47DAP	1.18409	0.414
57DAP/52DAP	1.53916	0.213
57DAP/7DAP	1.36866	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9169	0.168
17DAP/reference	0.937	0.016
27DAP/reference	0.87547	0.01
39DAP/reference	0.94063	0.023
41DAP/reference	0.95822	0.107
42DAP/reference	0.96842	0.222
43DAP/reference	0.85248	0.011
47DAP/reference	1.00535	1
52DAP/reference	0.82187	0.02
57DAP/reference	0.91372	0.026

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23627	0.319
17DAP/reference	1.7098	0.019
27DAP/reference	1.38976	0.017
39DAP/reference	1.63259	0.011
41DAP/reference	1.45279	0.005
42DAP/reference	1.47127	0.009
43DAP/reference	1.50366	0.101
47DAP/reference	1.34161	0.008
52DAP/reference	1.64411	0.006
57DAP/reference	1.87162	0.014

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90191	0.049
17DAP/reference	1.02922	0.814
27DAP/reference	0.90294	0.035
39DAP/reference	1.00554	0.889
41DAP/reference	1.06472	0.588
42DAP/reference	0.91992	0.361
43DAP/reference	1.20263	0.331
47DAP/reference	1.18409	0.309
52DAP/reference	0.87238	0.455
57DAP/reference	0.76749	0.1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09634	1
26DAP/20DAP	0.94484	1
34DAP/26DAP	1.48269	0.19
51DAP/34DAP	1.09314	0.637
52DAP/51DAP	1.15005	0.588
53DAP/52DAP	0.91884	0.649
55DAP/53DAP	1.13009	0.719
57DAP/55DAP	0.9668	0.825
62DAP/57DAP	0.85178	0.871
68DAP/62DAP	0.68757	0.429
68DAP/14DAP	0.55534	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.03026	0.855

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.69566	0.04
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.66577

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92152	0.944
1-1-2/M82	N/A	N/A
12-2/M82	1.10032
12-4/M82	1.0081	1
1-3/M82	0.89672
2-1-1/M82	1.75183
2-1/M82	N/A	N/A
2-6/M82	1.14116	0.405
3-2/M82	N/A	N/A
4-1-1/M82	0.95517	1
4-1/M82	0.9475
4-3-2/M82	0.89022
4-3/M82	0.93922	1
5-3/M82	0.93433	1
6-2/M82	1.20923
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.04942	0.299
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.11065	0.659
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.07394	1
IL12-4/WTpooled	0.91332	0.581
IL1-4/WTpooled	0.98345
WT/WTpooled	1.12168	0.957

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	0.90023	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97057	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.22993	1
DC3000/delta hrp 24h	1.10933	0.411

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.96602	1
DC3000 delta B/DC3000 delta AB	0.95954	0.674

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

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

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01013	1
Var 0h	1.35093	0.374
Var 12h I row2-row1	0.97856	1
Var 12h NI row2-row1	0.94831	0.906
Var 36h I row2-row1	0.96775	0.374
Var 36h NI row2-row1	1.0987	1
Var 60h I row2-row1	0.91335	0.439
Var 60h NI row2-row1	0.91818	0.69
Time course 0hI-0hNI	0.94393	0.6
Time course 12hI-12hNI	1.01427	0.833
Time course 36hI-36hNI	1.02648	0.975
Time course 60hI-60hNI	0.95823	0.319

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	0.59371	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.30065	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.92306	0.728