Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.7.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19988	0.523
27DAP/17DAP	0.74672	0.37
39DAP/27DAP	0.79795	0.397
41DAP/39DAP	0.84369	0.43
42DAP/41DAP	0.83328	1
43DAP/42DAP	1.03894	1
47DAP/43DAP	0.97421	0.876
52DAP/47DAP	0.84602	0.564
57DAP/52DAP	1.22531	0.853

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.59433	0.026
17DAP/reference	0.5565	0.009
27DAP/reference	0.73048	0.07
39DAP/reference	0.63914	0.017
41DAP/reference	0.45396	0.009
42DAP/reference	0.68781	0.001
43DAP/reference	0.74348	0.042
47DAP/reference	0.72846	0.003
52DAP/reference	0.72145	0.035
57DAP/reference	1.02606	0.829

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18024	0.121
27DAP/17DAP	0.91069	0.648
39DAP/27DAP	0.82482	0.088
41DAP/39DAP	1.08389	0.163
42DAP/41DAP	0.99186	0.869
43DAP/42DAP	0.99939	1
47DAP/43DAP	0.98703	0.939
52DAP/47DAP	1.13703	0.609
57DAP/52DAP	1.06752	0.584
57DAP/7DAP	0.95827	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95322	0.326
17DAP/reference	0.68359	0.011
27DAP/reference	0.51883	0.01
39DAP/reference	0.45916	0.011
41DAP/reference	0.50354	0.02
42DAP/reference	0.50056	0.012
43DAP/reference	0.35232	0.01
47DAP/reference	0.77275	0.293
52DAP/reference	0.37596	0.011
57DAP/reference	0.39036	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.45772	0.007
17DAP/reference	0.48664	0.01
27DAP/reference	0.82766	0.195
39DAP/reference	1.02487	0.722
41DAP/reference	1.14579	0.587
42DAP/reference	1.08135	0.777
43DAP/reference	0.41045	0.004
47DAP/reference	0.97597	0.487
52DAP/reference	0.80195	0.02
57DAP/reference	0.50481	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.83983	0.016
17DAP/reference	1.44658	0.376
27DAP/reference	1.20758	0.271
39DAP/reference	0.95395	0.43
41DAP/reference	0.74919	0.07
42DAP/reference	0.70109	0.108
43DAP/reference	0.62481	0.028
47DAP/reference	1.09205	0.731
52DAP/reference	1.18804	0.538
57DAP/reference	2.12624	0.027

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05306	1
26DAP/20DAP	0.97855	1
34DAP/26DAP	1.06644	0.819
51DAP/34DAP	0.76805	0.08
52DAP/51DAP	1.17385	0.075
53DAP/52DAP	0.91118	0.489
55DAP/53DAP	1.22419	0.295
57DAP/55DAP	0.84781	0.437
62DAP/57DAP	1.37105	0.868
68DAP/62DAP	4.4432	0.033
68DAP/14DAP	3.19473	0.023

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.7564	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	7.56027	0.058
Mature Green Tomato/Ripe Tomato	1.76721	0.134
Immature Eggplant/Mature Eggplant	0.26597	0.057
Ripe Pepper/Ripe Tomato	3.05193	0.258
Mature Eggplant/Ripe Tomato	16.0493	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.99364
12-2/M82	0.7891
12-4/M82	1.00601	1
1-3/M82	N/A	N/A
2-1-1/M82	0.78455
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	3.72933
4-1-1/M82	1.50072
4-1/M82	1.26047
4-3-2/M82	1.36001
4-3/M82	0.72717	0.551
5-3/M82	1.55809
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.17113
7-2/M82	N/A	N/A
9-3-2/M82	1.07231	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.31976	0.247
IL2-6/WTpooled	1.34491	0.584
IL7-5/WTpooled	1.0898	1
IL7-3/WTpooled	0.21106	0.25
IL12-4/WTpooled	0.64303	0.478
IL1-4/WTpooled	1.03563	1
WT/WTpooled	0.99616	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	1.07357	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95468
DC3000/delta hrp 6h	1.02351	1
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	1.08222	0.553

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.5969	0.024
DC3000 delta B/DC3000 delta AB	0.55187	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03558	1
Exp 36h	0.83566	0.661
Exp 60h	0.82798	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98999	1
Var 0h	0.798	1
Var 12h I row2-row1	0.86272	0.338
Var 12h NI row2-row1	0.97468	0.82
Var 36h I row2-row1	0.90662	0.805
Var 36h NI row2-row1	1.14695	0.482
Var 60h I row2-row1	1.31668	0.543
Var 60h NI row2-row1	1.00002	1
Time course 0hI-0hNI	0.98903	1
Time course 12hI-12hNI	1.04774	0.678
Time course 36hI-36hNI	1.08257	0.28
Time course 60hI-60hNI	0.23059	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)	1.08893	0.921
transgenic ySAMdc/azygous control (breaker)	2.10554	0.178
transgenic ySAMdc/azygous control (red)	1.50058	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.48065	0.078

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.25287	0.223

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	21.838	0.083
Manapal/WT (break)	4.87372	0.13
Manapal/WT (red)	2.61651	0.222