Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.12.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.70618	0.443
27DAP/17DAP	1.14936	0.895
39DAP/27DAP	1.86077	0.028
41DAP/39DAP	1.1054	0.894
42DAP/41DAP	1.12623	0.926
43DAP/42DAP	1.35482	0.937
47DAP/43DAP	1.84326	0.156
52DAP/47DAP	1.05865	0.845
57DAP/52DAP	1.63484	0.964

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.25783	0.065
17DAP/reference	0.93703	0.342
27DAP/reference	1.17351	0.415
39DAP/reference	1.01946	0.991
41DAP/reference	1.07983	0.855
42DAP/reference	1.8831	0.002
43DAP/reference	1.21014	0.019
47DAP/reference	1.9148	0.001
52DAP/reference	1.89672	0.007
57DAP/reference	1.54424	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.99519	0.148
27DAP/17DAP	1.13345	0.751
39DAP/27DAP	1.45664	0.076
41DAP/39DAP	0.68464	0.021
42DAP/41DAP	1.1801	0.263
43DAP/42DAP	0.89929	0.308
47DAP/43DAP	0.83688	0.086
52DAP/47DAP	1.75775	0.051
57DAP/52DAP	0.79629	0.082
57DAP/7DAP	1.82646	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84523	0.058
17DAP/reference	0.91183	0.094
27DAP/reference	1.12236	1
39DAP/reference	1.00359	0.745
41DAP/reference	1.05466	0.836
42DAP/reference	0.95411	0.393
43DAP/reference	0.88235	0.151
47DAP/reference	1.24865	0.026
52DAP/reference	0.87978	0.137
57DAP/reference	0.80726	0.015

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90684	0.353
17DAP/reference	1.13211	0.042
27DAP/reference	1.10015	0.38
39DAP/reference	1.16682	0.099
41DAP/reference	0.86024	0.148
42DAP/reference	1.16112	0.509
43DAP/reference	0.84267	0.147
47DAP/reference	1.25061	0.256
52DAP/reference	0.80032	0.017
57DAP/reference	0.93966	0.338

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88983	0.268
17DAP/reference	0.83335	0.144
27DAP/reference	0.86814	0.147
39DAP/reference	1.00203	0.889
41DAP/reference	0.96114	0.56
42DAP/reference	0.97501	0.671
43DAP/reference	1.08827	0.515
47DAP/reference	1.06115	0.501
52DAP/reference	1.26811	0.141
57DAP/reference	1.51797	0.029

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04646	1
26DAP/20DAP	0.6936	0.317
34DAP/26DAP	1.70578	0.19
51DAP/34DAP	0.83982	0.667
52DAP/51DAP	0.97472	1
53DAP/52DAP	1.2259	0.608
55DAP/53DAP	1.36531	0.917
57DAP/55DAP	1.05981	0.855
62DAP/57DAP	1.68648	0.723
68DAP/62DAP	1.24304	0.897
68DAP/14DAP	1.21345	0.739

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.12554	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.96852	0.058
Mature Green Tomato/Ripe Tomato	0.66969	0.096
Immature Eggplant/Mature Eggplant	0.9449	0.912
Ripe Pepper/Ripe Tomato	0.26829	0.224
Mature Eggplant/Ripe Tomato	0.35995	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.83371
1-1-2/M82	0.92445	1
12-2/M82	0.69462	0.74
12-4/M82	1.2282	1
1-3/M82	1.43928	0.248
2-1-1/M82	1.31914	1
2-1/M82	0.71603
2-6/M82	1.01051	1
3-2/M82	1.02116	1
4-1-1/M82	1.40904	0.977
4-1/M82	0.70893
4-3-2/M82	1.51982	1
4-3/M82	1.39867	1
5-3/M82	1.02127	1
6-2/M82	1.14796	1
6-3/M82	0.67209	0.397
7-1/M82	2.09894	0.598
7-2/M82	1.52431
9-3-2/M82	1.02252	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.87043	0.321
IL2-6/WTpooled	0.87639	0.358
IL7-5/WTpooled	1.101	1
IL7-3/WTpooled	1.3202	0.362
IL12-4/WTpooled	1.22826	0.516
IL1-4/WTpooled	1.01452	0.426
WT/WTpooled	0.93841	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	0.80538	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01579	1
DC3000/delta hrp 6h	1.19074	1
DC3000/delta hrp 12h	1.09249	1
DC3000/delta hrp 24h	0.49809	0.034

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	0.50514	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.92975	1
Exp 36h	0.66256	0.406
Exp 60h	0.6285	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	1.11965	1
Var 0h	1.00065	1
Var 12h I row2-row1	0.86559	0.357
Var 12h NI row2-row1	1.01065	1
Var 36h I row2-row1	0.93547
Var 36h NI row2-row1	1.06386	1
Var 60h I row2-row1	1.24547	0.389
Var 60h NI row2-row1	0.97021	1
Time course 0hI-0hNI	1.06845	0.833
Time course 12hI-12hNI	0.88461	0.338
Time course 36hI-36hNI	0.82088	0.076
Time course 60hI-60hNI	0.75479	0.047

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)	1.03046	0.798
transgenic ySAMdc/azygous control (breaker)	1.55808	0.166
transgenic ySAMdc/azygous control (red)	0.8022	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.2082	0.125

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.29978	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.15885	0.14
Manapal/WT (break)	1.61962	0.14
Manapal/WT (red)	2.424	0.126