Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.8.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10977	0.656
27DAP/17DAP	1.0876	0.881
39DAP/27DAP	0.90943	0.522
41DAP/39DAP	1.02996	0.753
42DAP/41DAP	0.92739	1
43DAP/42DAP	1.16095	0.873
47DAP/43DAP	1.02745	0.999
52DAP/47DAP	0.92753	0.777
57DAP/52DAP	0.94722	0.919

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94187	0.254
17DAP/reference	0.93353	0.18
27DAP/reference	0.93343	0.129
39DAP/reference	0.93732	0.324
41DAP/reference	0.99076	0.667
42DAP/reference	1.04179	0.366
43DAP/reference	1.00982	0.928
47DAP/reference	1.02246	0.593
52DAP/reference	0.96239	0.405
57DAP/reference	1.06037	0.643

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98367	0.697
27DAP/17DAP	0.94889	0.887
39DAP/27DAP	1.02798	0.698
41DAP/39DAP	1.01771	0.849
42DAP/41DAP	1.0081	1
43DAP/42DAP	1.07037	0.324
47DAP/43DAP	1.01536	0.93
52DAP/47DAP	0.98455	0.93
57DAP/52DAP	1.00268	1
57DAP/7DAP	1.05127	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93394	0.168
17DAP/reference	0.91318	0.072
27DAP/reference	0.9189	0.02
39DAP/reference	0.86209	0.011
41DAP/reference	0.93789	0.056
42DAP/reference	0.82653	0.01
43DAP/reference	0.87427	0.012
47DAP/reference	0.91767	0.079
52DAP/reference	0.81429	0.012
57DAP/reference	0.73171	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98491	0.72
17DAP/reference	1.02059	0.806
27DAP/reference	0.98627	0.576
39DAP/reference	0.93078	0.298
41DAP/reference	0.90952	0.152
42DAP/reference	0.94379	0.289
43DAP/reference	0.96165	0.438
47DAP/reference	1.04956	0.098
52DAP/reference	0.93783	0.143
57DAP/reference	1.01785	0.771

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88724	0.068
17DAP/reference	0.9022	0.135
27DAP/reference	0.89222	0.038
39DAP/reference	0.87209	0.012
41DAP/reference	0.90395	0.032
42DAP/reference	0.9049	0.134
43DAP/reference	1.02495	0.79
47DAP/reference	0.94695	0.224
52DAP/reference	0.88301	0.262
57DAP/reference	0.92369	0.167

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04403	0.85
26DAP/20DAP	0.99677	1
34DAP/26DAP	1.01069	1
51DAP/34DAP	1.02163	0.829
52DAP/51DAP	0.9221	0.07
53DAP/52DAP	1.16555
55DAP/53DAP	0.92983	0.233
57DAP/55DAP	1.15908	0.461
62DAP/57DAP	1.11365	0.8
68DAP/62DAP	1.33864	0.864
68DAP/14DAP	1.17148	0.279

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.00015	0.814

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.52972	0.111
Mature Green Tomato/Ripe Tomato	0.86234	0.2
Immature Eggplant/Mature Eggplant	1.02051	1
Ripe Pepper/Ripe Tomato	3.813	1
Mature Eggplant/Ripe Tomato	1.56345	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99928	1
1-1-2/M82	1.02596	1
12-2/M82	0.94538	0.955
12-4/M82	0.99291	1
1-3/M82	0.96725	0.501
2-1-1/M82	0.83907	0.465
2-1/M82	0.89701	1
2-6/M82	0.97224	0.501
3-2/M82	0.94455	1
4-1-1/M82	1.03577	1
4-1/M82	1.04736	1
4-3-2/M82	0.7412	0.297
4-3/M82	0.90873	0.72
5-3/M82	1.07468	0.572
6-2/M82	0.9775	1
6-3/M82	1.06501	1
7-1/M82	1.00805	1
7-2/M82	0.94618	0.881
9-3-2/M82	0.82994	0.449

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	1.11712
IL12-4/WTpooled	0.75645	0.581
IL1-4/WTpooled	0.98773	1
WT/WTpooled	0.90448	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	0.89056	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95793	1
DC3000/delta hrp 6h	1.3481	1
DC3000/delta hrp 12h	0.91648	1
DC3000/delta hrp 24h	1.05778	0.535

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.05178	0.355
DC3000 delta B/DC3000 delta AB	1.09172	0.336

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94163	1
Exp 36h	N/A	N/A
Exp 60h	0.9576	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9945	1
Var 0h	0.99357	1
Var 12h I row2-row1	1.09472	0.544
Var 12h NI row2-row1	0.8836	0.627
Var 36h I row2-row1	0.79886	1
Var 36h NI row2-row1	1.12726	0.482
Var 60h I row2-row1	1.21524	0.562
Var 60h NI row2-row1	1.21679	0.904
Time course 0hI-0hNI	1.10111	0.764
Time course 12hI-12hNI	1.00737	1
Time course 36hI-36hNI	0.98955	0.654
Time course 60hI-60hNI	1.1671	0.033

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)	0.96109	0.567
transgenic ySAMdc/azygous control (breaker)	1.56697	0.248
transgenic ySAMdc/azygous control (red)	1.39552	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.92549	0.046

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.19616	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.72641	0.084
Manapal/WT (break)	2.51546	0.381
Manapal/WT (red)	2.81684	0.142