Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.4.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07065	0.812
27DAP/17DAP	1.09251	0.885
39DAP/27DAP	0.71717	0.222
41DAP/39DAP	1.18518	0.37
42DAP/41DAP	0.93694	1
43DAP/42DAP	0.97826	0.918
47DAP/43DAP	1.23696	0.349
52DAP/47DAP	0.78388	0.466
57DAP/52DAP	0.98902	0.982

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84532	0.029
17DAP/reference	0.90005	0.138
27DAP/reference	1.06832	0.569
39DAP/reference	1.0354	0.311
41DAP/reference	0.86828	0.201
42DAP/reference	0.98088	0.337
43DAP/reference	0.95354	0.48
47DAP/reference	1.08058	0.19
52DAP/reference	1.11172	0.354
57DAP/reference	1.06392	0.984

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95368	0.595
27DAP/17DAP	1.22708	0.393
39DAP/27DAP	1.15784	0.388
41DAP/39DAP	0.961	0.945
42DAP/41DAP	1.02304	1
43DAP/42DAP	1.11169	0.554
47DAP/43DAP	0.9442	0.569
52DAP/47DAP	1.06543	0.785
57DAP/52DAP	1.12738	0.466
57DAP/7DAP	1.33254	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06906	0.732
17DAP/reference	0.93886	0.295
27DAP/reference	1.02838	1
39DAP/reference	1.0349	1
41DAP/reference	0.90244	0.184
42DAP/reference	1.01486	1
43DAP/reference	1.08081	0.483
47DAP/reference	1.08164	0.537
52DAP/reference	0.86919	0.066
57DAP/reference	0.90307	0.162

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74254	0.034
17DAP/reference	0.84309	0.025
27DAP/reference	0.81626	0.115
39DAP/reference	0.81537	0.095
41DAP/reference	1.04732	1
42DAP/reference	0.96867	0.482
43DAP/reference	1.019	0.692
47DAP/reference	0.98262	0.543
52DAP/reference	0.95173	0.38
57DAP/reference	0.89213	0.169

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86368	0.311
17DAP/reference	0.885	0.186
27DAP/reference	0.89431	0.133
39DAP/reference	0.9637	0.464
41DAP/reference	0.86128	0.119
42DAP/reference	0.94132	0.361
43DAP/reference	0.98358	0.639
47DAP/reference	1.0689	0.48
52DAP/reference	1.28106	0.448
57DAP/reference	1.16857	0.126

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08047	1
26DAP/20DAP	0.92988	0.512
34DAP/26DAP	1.03706	1
51DAP/34DAP	1.089	0.597
52DAP/51DAP	0.93141	1
53DAP/52DAP	1.04166	0.921
55DAP/53DAP	1.00461	0.894
57DAP/55DAP	1.03628	1
62DAP/57DAP	1.50359	0.569
68DAP/62DAP	0.91097	0.505
68DAP/14DAP	1.04298	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.17981	0.122

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.1524	0.058
Mature Green Tomato/Ripe Tomato	1.09452	1
Immature Eggplant/Mature Eggplant	0.52876	0.079
Ripe Pepper/Ripe Tomato	0.39616	0.293
Mature Eggplant/Ripe Tomato	0.69173	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00434	1
1-1-2/M82	1.08506	1
12-2/M82	0.97596	1
12-4/M82	0.97284	0.619
1-3/M82	0.80078
2-1-1/M82	1.18751	0.764
2-1/M82	0.8467
2-6/M82	0.97607	1
3-2/M82	1.00446	1
4-1-1/M82	1.13171	0.968
4-1/M82	0.92677	1
4-3-2/M82	1.02511	1
4-3/M82	1.0512	1
5-3/M82	0.95739	1
6-2/M82	1.05603
6-3/M82	0.97658	1
7-1/M82	0.90631	1
7-2/M82	0.97923	1
9-3-2/M82	1.10707	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	N/A	N/A
IL12-4/WTpooled	0.56219
IL1-4/WTpooled	1.07122
WT/WTpooled	1.05689	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	1.00891	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.14553	0.25
DC3000/delta hrp 6h	1.05287	0.95
DC3000/delta hrp 12h	0.9788	1
DC3000/delta hrp 24h	0.9701	0.794

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.72642	0.629
DC3000 delta B/DC3000 delta AB	0.94554	0.638

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01804	1
Exp 36h	0.83398	0.623
Exp 60h	0.95752	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.98647	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.1111	0.221
transgenic ySAMdc/azygous control (breaker)	1.00788	1
transgenic ySAMdc/azygous control (red)	1.03203	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99571	0.737

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95917	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.76378	1
Manapal/WT (break)	0.82976	1
Manapal/WT (red)	1.15018	0.413