Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.2.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.36663	0.428
27DAP/17DAP	0.81804	0.496
39DAP/27DAP	1.29189	0.588
41DAP/39DAP	1.04533	0.958
42DAP/41DAP	1.0279	1
43DAP/42DAP	1.04173	1
47DAP/43DAP	0.89533	0.634
52DAP/47DAP	1.14643	0.787
57DAP/52DAP	1.40314	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.40069	0.025
17DAP/reference	1.31669	0.161
27DAP/reference	2.33867	0.008
39DAP/reference	2.07692	0.162
41DAP/reference	1.25352	0.241
42DAP/reference	2.9767	0.001
43DAP/reference	3.02326	0.008
47DAP/reference	5.0308	0.001
52DAP/reference	2.3014	0.016
57DAP/reference	1.90727	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.53106	0.036
27DAP/17DAP	1.13685	0.831
39DAP/27DAP	1.39747	0.429
41DAP/39DAP	1.18321	0.799
42DAP/41DAP	1.05687	0.893
43DAP/42DAP	0.84838	0.085
47DAP/43DAP	0.95474	0.796
52DAP/47DAP	1.00575	0.97
57DAP/52DAP	1.29306	0.405
57DAP/7DAP	1.09276	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03513	0.758
17DAP/reference	0.86374	0.072
27DAP/reference	1.08936	0.664
39DAP/reference	0.97109	0.474
41DAP/reference	1.40879	0.791
42DAP/reference	1.02392	0.889
43DAP/reference	1.30821	0.111
47DAP/reference	2.76968	0.039
52DAP/reference	0.90047	0.066
57DAP/reference	0.96626	0.443

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.25949	0.005
17DAP/reference	2.24782	0.01
27DAP/reference	3.30812	0.012
39DAP/reference	3.10877	0.011
41DAP/reference	4.27872	0.004
42DAP/reference	4.15325	0.007
43DAP/reference	1.36802	0.91
47DAP/reference	2.63171	0.008
52DAP/reference	2.42244	0.006
57DAP/reference	1.14082	0.916

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1864	0.311
17DAP/reference	1.09227	0.833
27DAP/reference	1.02811	1
39DAP/reference	1.39576	0.043
41DAP/reference	1.14616	0.537
42DAP/reference	1.62548	0.214
43DAP/reference	3.7583	0.107
47DAP/reference	4.54283	0.005
52DAP/reference	3.6754	0.209
57DAP/reference	9.50688	0.009

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.18719	0.966
26DAP/20DAP	1.37563	0.192
34DAP/26DAP	1.06589	1
51DAP/34DAP	1.03944	0.967
52DAP/51DAP	1.10077	0.467
53DAP/52DAP	1.27003	0.082
55DAP/53DAP	1.461	0.555
57DAP/55DAP	0.87757	0.532
62DAP/57DAP	0.83371	0.681
68DAP/62DAP	1.48632	0.118
68DAP/14DAP	0.78391	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.81248	0.097

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.31138	0.068
Mature Green Tomato/Ripe Tomato	1.22518	1
Immature Eggplant/Mature Eggplant	0.71448	0.159
Ripe Pepper/Ripe Tomato	0.27449	0.224
Mature Eggplant/Ripe Tomato	0.22086	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.85109	0.605
1-1-2/M82	1.18775	1
12-2/M82	1.02147	1
12-4/M82	0.93761	1
1-3/M82	1.34746	1
2-1-1/M82	0.73187	0.683
2-1/M82	0.69131	0.322
2-6/M82	0.8777	1
3-2/M82	1.0793
4-1-1/M82	0.77287	1
4-1/M82	0.83642
4-3-2/M82	0.83968	1
4-3/M82	1.08854	1
5-3/M82	1.05833	1
6-2/M82	0.91097	1
6-3/M82	0.92468	1
7-1/M82	1.00001	1
7-2/M82	1.03774	1
9-3-2/M82	0.98373

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.06098	1
IL2-6/WTpooled	1.14662	0.415
IL7-5/WTpooled	0.66677
IL7-3/WTpooled	0.95286	0.418
IL12-4/WTpooled	0.95242	0.71
IL1-4/WTpooled	1.13204	1
WT/WTpooled	0.97171	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	1.15139	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92557	1
DC3000/delta hrp 6h	0.98315	0.95
DC3000/delta hrp 12h	1.03059	1
DC3000/delta hrp 24h	1.47991	0.107

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.66424	0.074
DC3000 delta B/DC3000 delta AB	1.05557	0.516

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96241	0.328
Exp 36h	1.16562	0.371
Exp 60h	1.30625	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98386	1
Var 0h	2.27957	0.98
Var 12h I row2-row1	0.92554	0.705
Var 12h NI row2-row1	1.12947	0.649
Var 36h I row2-row1	0.99229	1
Var 36h NI row2-row1	1.0398	1
Var 60h I row2-row1	0.82046	0.306
Var 60h NI row2-row1	1.0644	1
Time course 0hI-0hNI	0.99868	1
Time course 12hI-12hNI	0.99188	0.994
Time course 36hI-36hNI	1.01676	1
Time course 60hI-60hNI	0.62865	0.006

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)	1.07228	0.571
transgenic ySAMdc/azygous control (breaker)	0.68978	0.15
transgenic ySAMdc/azygous control (red)	0.88154	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.45084	0.026

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.71728	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.87325	1
Manapal/WT (break)	0.79349	0.333
Manapal/WT (red)	1.13482	1