Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.5.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92008	0.652
27DAP/17DAP	0.87368	0.686
39DAP/27DAP	0.87492	0.397
41DAP/39DAP	1.05793	0.822
42DAP/41DAP	1.03023	0.999
43DAP/42DAP	1.03374	1
47DAP/43DAP	1.06904	0.842
52DAP/47DAP	0.85165	0.607
57DAP/52DAP	1.11521	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.30988	0.025
17DAP/reference	0.44643	0.009
27DAP/reference	0.50187	0.016
39DAP/reference	0.60863	0.023
41DAP/reference	0.53304	0.026
42DAP/reference	0.51624	0.001
43DAP/reference	0.73952	0.135
47DAP/reference	0.54184	0.001
52DAP/reference	0.47979	0.028
57DAP/reference	0.92422	0.186

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94716	0.613
27DAP/17DAP	0.96457	0.854
39DAP/27DAP	1.24947	0.171
41DAP/39DAP	1.14199	0.65
42DAP/41DAP	0.97159	0.751
43DAP/42DAP	0.82243	0.025
47DAP/43DAP	1.10184	0.681
52DAP/47DAP	1.21212	0.558
57DAP/52DAP	0.93577	0.608
57DAP/7DAP	0.89614	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.54189	0.05
17DAP/reference	0.55632	0.011
27DAP/reference	0.60259	0.023
39DAP/reference	0.47744	0.011
41DAP/reference	0.53854	0.009
42DAP/reference	0.52415	0.01
43DAP/reference	0.52578	0.01
47DAP/reference	0.54442	0.036
52DAP/reference	0.41157	0.012
57DAP/reference	0.44379	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.28492	0.005
17DAP/reference	0.30479	0.004
27DAP/reference	0.5328	0.048
39DAP/reference	0.37624	0.008
41DAP/reference	0.52897	0.027
42DAP/reference	0.52214	0.01
43DAP/reference	0.53747	0.006
47DAP/reference	0.52447	0.009
52DAP/reference	0.32473	0.003
57DAP/reference	0.34951	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.50458	0.032
17DAP/reference	0.59331	0.102
27DAP/reference	0.45131	0.021
39DAP/reference	0.4439	0.008
41DAP/reference	0.51588	0.019
42DAP/reference	0.5403	0.016
43DAP/reference	0.57599	0.017
47DAP/reference	0.41482	0.005
52DAP/reference	0.84365	0.216
57DAP/reference	0.55889	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95872	1
26DAP/20DAP	1.29262	0.66
34DAP/26DAP	1.0697	1
51DAP/34DAP	1.30864	0.925
52DAP/51DAP	0.84638	1
53DAP/52DAP	0.72084	0.117
55DAP/53DAP	1.04546	0.894
57DAP/55DAP	1.0213	1
62DAP/57DAP	1.0099	1
68DAP/62DAP	1.05964
68DAP/14DAP	1.02959	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.61744	0.052

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.34316	0.106
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.50132
12-2/M82	N/A	N/A
12-4/M82	0.71573
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.99977
4-1-1/M82	N/A	N/A
4-1/M82	0.99601	1
4-3-2/M82	0.96741
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.8275
7-2/M82	N/A	N/A
9-3-2/M82	0.9352	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.98049	1
IL2-6/WTpooled	0.80844	0.473
IL7-5/WTpooled	0.93233	1
IL7-3/WTpooled	0.91802	0.418
IL12-4/WTpooled	1.02673	0.785
IL1-4/WTpooled	1.0316	1
WT/WTpooled	1.02658	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	1.06877	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.49859
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.81509
DC3000/delta hrp 24h	2.54116	0.03

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	1.6854	0.315

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	1.44922	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99065	1
Var 0h	0.91567	0.933
Var 12h I row2-row1	1.00987	1
Var 12h NI row2-row1	0.89949	0.906
Var 36h I row2-row1	0.89612	0.805
Var 36h NI row2-row1	1.12606	1
Var 60h I row2-row1	0.76063	0.374
Var 60h NI row2-row1	0.87666	0.69
Time course 0hI-0hNI	0.90646	0.241
Time course 12hI-12hNI	1.00125	1
Time course 36hI-36hNI	0.94737	0.418
Time course 60hI-60hNI	0.86569	0.026

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)	1.18784	0.862
transgenic ySAMdc/azygous control (breaker)	1.15602	1
transgenic ySAMdc/azygous control (red)	1.00514	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98852	0.517

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.44589	0.277

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)	0.964	1
Manapal/WT (red)	N/A	N/A