Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-3.4.16.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96647	0.752
27DAP/17DAP	1.01261	0.941
39DAP/27DAP	1.62943	0.102
41DAP/39DAP	0.74863	0.169
42DAP/41DAP	1.1276	0.886
43DAP/42DAP	1.00657	0.937
47DAP/43DAP	1.31192	0.391
52DAP/47DAP	0.84248	0.595
57DAP/52DAP	1.42095	0.837

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14089	0.218
17DAP/reference	0.84956	0.069
27DAP/reference	0.84111	0.028
39DAP/reference	0.91665	0.228
41DAP/reference	0.78282	0.031
42DAP/reference	1.15085	0.004
43DAP/reference	1.01893	0.838
47DAP/reference	1.26502	0.001
52DAP/reference	1.41125	0.021
57DAP/reference	1.38508	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01253	0.899
27DAP/17DAP	1.24469	0.161
39DAP/27DAP	1.00168	1
41DAP/39DAP	1.00623	1
42DAP/41DAP	0.99153	0.835
43DAP/42DAP	1.01998	0.83
47DAP/43DAP	1.0882	0.563
52DAP/47DAP	0.87041	0.29
57DAP/52DAP	1.13203	0.596
57DAP/7DAP	0.77214	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24931	0.048
17DAP/reference	0.99252	0.599
27DAP/reference	1.0901	0.16
39DAP/reference	1.01062	1
41DAP/reference	0.9856	0.589
42DAP/reference	1.07885	0.889
43DAP/reference	0.98669	0.555
47DAP/reference	1.194	0.112
52DAP/reference	1.05362	0.732
57DAP/reference	1.09417	0.382

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07805	0.577
17DAP/reference	0.99623	0.766
27DAP/reference	0.99954	0.79
39DAP/reference	1.07884	0.529
41DAP/reference	0.9655	0.364
42DAP/reference	1.16378	0.064
43DAP/reference	0.88271	0.224
47DAP/reference	1.17617	0.108
52DAP/reference	0.80901	0.006
57DAP/reference	0.84714	0.073

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06326	0.377
17DAP/reference	0.97322	0.624
27DAP/reference	0.99398	0.727
39DAP/reference	1.08204	0.466
41DAP/reference	0.91258	0.417
42DAP/reference	1.10368	0.424
43DAP/reference	1.37337	0.024
47DAP/reference	0.98281	0.538
52DAP/reference	1.39753	0.055
57DAP/reference	1.85094	0.012

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94638	1
26DAP/20DAP	1.12171	1
34DAP/26DAP	1.95958	0.542
51DAP/34DAP	0.91329	0.743
52DAP/51DAP	0.96761	1
53DAP/52DAP	1.14473	0.83
55DAP/53DAP	0.89351	0.544
57DAP/55DAP	0.88271	0.577
62DAP/57DAP	0.80732	0.162
68DAP/62DAP	1.41759	0.682
68DAP/14DAP	1.54279	0.119

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	5.02602	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.03007	1
Mature Green Tomato/Ripe Tomato	0.94178	0.611
Immature Eggplant/Mature Eggplant	1.36947	0.054
Ripe Pepper/Ripe Tomato	0.63056	1
Mature Eggplant/Ripe Tomato	0.4203	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.59483	N/A
12-2/M82	N/A	N/A
12-4/M82	0.90515	N/A
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	1.07018	0.463
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.99112	N/A
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	0.83332	N/A
7-2/M82	0.91331	N/A
9-3-2/M82	1.33671	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	0.70257	0.298
IL12-4/WTpooled	1.05251	1
IL1-4/WTpooled	2.51808	1
WT/WTpooled	1.2184	0.999

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	1.26833	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.15706	0.894
DC3000/delta hrp 6h	0.86189	0.95
DC3000/delta hrp 12h	1.03345	1
DC3000/delta hrp 24h	1.0383	0.567

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.19147	0.29
DC3000 delta B/DC3000 delta AB	1.48234	0.079

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0041	1
Exp 36h	1.46558	0.693
Exp 60h	1.72763	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04106	1
Var 0h	0.39	1
Var 12h I row2-row1	0.99058	1
Var 12h NI row2-row1	1.0866	1
Var 36h I row2-row1	1.11858	0.908
Var 36h NI row2-row1	0.76246	0.329
Var 60h I row2-row1	1.00416	1
Var 60h NI row2-row1	0.81986	0.458
Time course 0hI-0hNI	0.91058	0.319
Time course 12hI-12hNI	1.06617	0.554
Time course 36hI-36hNI	1.59555	0.005
Time course 60hI-60hNI	1.56832	0.009

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)	1.05148	0.297
transgenic ySAMdc/azygous control (breaker)	1.18995	1
transgenic ySAMdc/azygous control (red)	1.13214	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08046	0.17

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.82004	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.02378	1
Manapal/WT (break)	1.19007	0.381
Manapal/WT (red)	1.31722	0.413