Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.20.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12235	0.932
27DAP/17DAP	1.13324	0.872
39DAP/27DAP	1.06593	0.857
41DAP/39DAP	0.99303	0.935
42DAP/41DAP	1.37351	0.366
43DAP/42DAP	0.92819	0.858
47DAP/43DAP	1.62725	0.563
52DAP/47DAP	1.28173	0.96
57DAP/52DAP	0.94242	0.932

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91297	0.238
17DAP/reference	0.9672	0.474
27DAP/reference	0.9935	0.797
39DAP/reference	0.90877	0.292
41DAP/reference	0.66602	0.009
42DAP/reference	0.91403	0.043
43DAP/reference	1.02128	0.924
47DAP/reference	1.13212	0.081
52DAP/reference	1.15486	0.134
57DAP/reference	1.06227	0.662

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.52855	0.5
27DAP/17DAP	1.85086	0.061
39DAP/27DAP	1.2092	0.587
41DAP/39DAP	0.70618	0.027
42DAP/41DAP	0.89186	0.402
43DAP/42DAP	1.15305	0.413
47DAP/43DAP	1.17053	0.108
52DAP/47DAP	0.74965	0.439
57DAP/52DAP	1.34478	0.402
57DAP/7DAP	1.13112	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88263	0.157
17DAP/reference	0.82792	0.025
27DAP/reference	0.98424	0.53
39DAP/reference	0.85544	0.031
41DAP/reference	0.91207	0.111
42DAP/reference	0.89618	0.05
43DAP/reference	0.91614	0.069
47DAP/reference	1.00121	1
52DAP/reference	0.81114	0.014
57DAP/reference	0.94867	0.328

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81834	0.06
17DAP/reference	0.81539	0.019
27DAP/reference	0.82923	0.144
39DAP/reference	0.91574	0.152
41DAP/reference	0.8194	0.067
42DAP/reference	0.96474	0.392
43DAP/reference	0.87613	0.236
47DAP/reference	0.88735	0.133
52DAP/reference	0.90348	0.111
57DAP/reference	0.70849	0.011

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85508	0.082
17DAP/reference	1.656	0.72
27DAP/reference	0.93616	0.286
39DAP/reference	0.8415	0.006
41DAP/reference	0.86987	0.055
42DAP/reference	1.07892	0.961
43DAP/reference	0.84157	0.031
47DAP/reference	1.11086	0.355
52DAP/reference	0.92051	0.482
57DAP/reference	1.19934	0.255

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.13404	1
26DAP/20DAP	1.4928	0.122
34DAP/26DAP	0.78929	0.186
51DAP/34DAP	1.28071	0.402
52DAP/51DAP	0.97743	1
53DAP/52DAP	2.37776	0.086
55DAP/53DAP	0.84843	0.293
57DAP/55DAP	0.94138	0.698
62DAP/57DAP	0.86473	0.681
68DAP/62DAP	1.66626	0.095
68DAP/14DAP	2.00156	0.018

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.69314	0.102

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.95408	0.648
Mature Green Tomato/Ripe Tomato	0.84792	0.226
Immature Eggplant/Mature Eggplant	0.83759	0.105
Ripe Pepper/Ripe Tomato	0.67025	0.293
Mature Eggplant/Ripe Tomato	0.50263	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	3.2059
1-1-2/M82	1.04977	1
12-2/M82	0.96204
12-4/M82	0.89737
1-3/M82	N/A	N/A
2-1-1/M82	0.60318
2-1/M82	1.27216	1
2-6/M82	N/A	N/A
3-2/M82	0.67572
4-1-1/M82	1.34655	1
4-1/M82	N/A	N/A
4-3-2/M82	0.67101
4-3/M82	3.69239	1
5-3/M82	1.14136	1
6-2/M82	1.11439
6-3/M82	1.28424	1
7-1/M82	0.95341
7-2/M82	2.05127	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.77431	0.247
IL2-6/WTpooled	0.83769	1
IL7-5/WTpooled	1.18425	0.792
IL7-3/WTpooled	1.2166	1
IL12-4/WTpooled	1.00828	0.839
IL1-4/WTpooled	0.92284	0.834
WT/WTpooled	1.02261	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	0.88018	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06277	0.921
DC3000/delta hrp 6h	0.98152	0.95
DC3000/delta hrp 12h	0.89226	1
DC3000/delta hrp 24h	0.60842	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.09749	0.441
DC3000 delta B/DC3000 delta AB	1.06874	0.579

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9922	1
Exp 36h	1.08681	1
Exp 60h	1.06079	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97568	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.37209	0.224
Var 12h NI row2-row1	0.98379	0.546
Var 36h I row2-row1	0.8842
Var 36h NI row2-row1	1.61429	0.11
Var 60h I row2-row1	0.99833
Var 60h NI row2-row1	1.36991	0.904
Time course 0hI-0hNI	0.9793	0.922
Time course 12hI-12hNI	1.15355	0.554
Time course 36hI-36hNI	0.71846	0.023
Time course 60hI-60hNI	0.38744	0.011

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)	1.03291	0.654
transgenic ySAMdc/azygous control (breaker)	0.92171	0.49
transgenic ySAMdc/azygous control (red)	1.04748	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.10325	0.448

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.84501	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.90204	1
Manapal/WT (break)	0.83699	0.333
Manapal/WT (red)	0.62007	0.181