Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.11.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09636	0.911
27DAP/17DAP	1.24755	0.755
39DAP/27DAP	1.34339	0.219
41DAP/39DAP	0.90771	0.611
42DAP/41DAP	1.15064	0.751
43DAP/42DAP	1.05818	1
47DAP/43DAP	1.3484	0.355
52DAP/47DAP	1.05327	0.937
57DAP/52DAP	1.21446	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93479	0.284
17DAP/reference	1.14662	0.061
27DAP/reference	1.1845	0.103
39DAP/reference	1.26655	0.018
41DAP/reference	1.10036	0.516
42DAP/reference	1.13891	0.166
43DAP/reference	1.31239	0.012
47DAP/reference	1.66582	0.001
52DAP/reference	1.41402	0.01
57DAP/reference	1.19123	0.122

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10189	0.961
27DAP/17DAP	1.17935	0.5
39DAP/27DAP	1.15127	0.429
41DAP/39DAP	0.91797	0.747
42DAP/41DAP	1.47498	0.401
43DAP/42DAP	0.99636	0.991
47DAP/43DAP	1.01507	0.941
52DAP/47DAP	1.07518	0.819
57DAP/52DAP	0.97713	0.776
57DAP/7DAP	0.98877	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12188	0.173
17DAP/reference	1.32294	0.022
27DAP/reference	1.28459	0.01
39DAP/reference	1.37703	0.007
41DAP/reference	1.0877	0.475
42DAP/reference	1.16148	0.037
43DAP/reference	1.32256	0.02
47DAP/reference	1.38662	0.039
52DAP/reference	1.18577	0.247
57DAP/reference	1.22488	0.037

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85771	0.129
17DAP/reference	1.04721	0.756
27DAP/reference	1.05533	0.735
39DAP/reference	0.99814	0.661
41DAP/reference	0.94491	0.357
42DAP/reference	0.94003	0.212
43DAP/reference	0.87332	0.077
47DAP/reference	1.03564	0.658
52DAP/reference	0.83408	0.023
57DAP/reference	0.92842	0.298

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94548	0.362
17DAP/reference	0.89501	0.262
27DAP/reference	1.14264	0.227
39DAP/reference	1.21959	0.016
41DAP/reference	1.07743	0.411
42DAP/reference	1.38803	0.08
43DAP/reference	1.31329	0.022
47DAP/reference	1.35919	0.006
52DAP/reference	2.0226	0.029
57DAP/reference	1.45669	0.029

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08748	0.966
26DAP/20DAP	1.5144	0.13
34DAP/26DAP	1.10808	0.542
51DAP/34DAP	1.30517	0.339
52DAP/51DAP	1.07023	0.708
53DAP/52DAP	0.94978	0.79
55DAP/53DAP	0.89782	0.53
57DAP/55DAP	1.10376	0.955
62DAP/57DAP	0.91097	0.681
68DAP/62DAP	0.88555	0.641
68DAP/14DAP	0.87895	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.77646	0.016

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.07736	0.666
Mature Green Tomato/Ripe Tomato	0.68663	0.047
Immature Eggplant/Mature Eggplant	1.0949	0.363
Ripe Pepper/Ripe Tomato	0.49801	0.224
Mature Eggplant/Ripe Tomato	0.64447	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97743	0.961
1-1-2/M82	1.30612	1
12-2/M82	1.03238	1
12-4/M82	0.92087	0.282
1-3/M82	1.83171	0.26
2-1-1/M82	1.15309	0.764
2-1/M82	0.66316	0.345
2-6/M82	1.07211	0.695
3-2/M82	1.01576	1
4-1-1/M82	1.1031	1
4-1/M82	1.25926	1
4-3-2/M82	1.16495	0.508
4-3/M82	1.31634	1
5-3/M82	1.0692	1
6-2/M82	0.93247	1
6-3/M82	1.00714	1
7-1/M82	0.84193	0.803
7-2/M82	1.16307	0.385
9-3-2/M82	1.20583	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
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	1.14996	0.084

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.17127
DC3000/delta hrp 6h	1.13082	1
DC3000/delta hrp 12h	0.90717	1
DC3000/delta hrp 24h	1.13931	0.221

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.37731	0.229
DC3000 delta B/DC3000 delta AB	1.2907	0.137

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.12928	1
Exp 36h	1.02408	1
Exp 60h	1.15925	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98201	1
Var 0h	0.85713	0.933
Var 12h I row2-row1	0.96595	0.77
Var 12h NI row2-row1	1.13379	0.649
Var 36h I row2-row1	1.07533	1
Var 36h NI row2-row1	0.94411	0.706
Var 60h I row2-row1	0.88024	0.287
Var 60h NI row2-row1	0.8879	0.516
Time course 0hI-0hNI	0.97843	0.911
Time course 12hI-12hNI	1.00199	1
Time course 36hI-36hNI	1.14183	0.355
Time course 60hI-60hNI	1.71004	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)	1.00797	0.921
transgenic ySAMdc/azygous control (breaker)	0.79521	0.15
transgenic ySAMdc/azygous control (red)	1.00272	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03065	0.687

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.68848	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.85228	1
Manapal/WT (break)	0.928	1
Manapal/WT (red)	0.95751	0.503