Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.12.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9859	0.847
27DAP/17DAP	0.94068	0.81
39DAP/27DAP	1.17494	0.713
41DAP/39DAP	0.85813	0.457
42DAP/41DAP	0.93375	1
43DAP/42DAP	1.06668	1
47DAP/43DAP	1.05996	0.889
52DAP/47DAP	1.09989	0.989
57DAP/52DAP	0.76371	0.506

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03152	0.662
17DAP/reference	0.97131	0.321
27DAP/reference	1.00489	0.966
39DAP/reference	1.00996	0.828
41DAP/reference	0.96014	0.201
42DAP/reference	0.93378	0.021
43DAP/reference	1.00447	0.982
47DAP/reference	0.96272	0.242
52DAP/reference	0.99445	0.709
57DAP/reference	0.93611	0.147

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07096	0.29
27DAP/17DAP	0.89856	0.187
39DAP/27DAP	0.76729	0.059
41DAP/39DAP	1.0834	0.656
42DAP/41DAP	0.88983	0.214
43DAP/42DAP	0.89705	0.197
47DAP/43DAP	1.0906	0.432
52DAP/47DAP	0.8954	0.446
57DAP/52DAP	0.80369	0.113
57DAP/7DAP	0.68501	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98454	0.55
17DAP/reference	0.99131	0.599
27DAP/reference	0.86538	0.01
39DAP/reference	0.98681	0.411
41DAP/reference	0.82373	0.012
42DAP/reference	0.77963	0.01
43DAP/reference	0.81023	0.013
47DAP/reference	0.94416	0.504
52DAP/reference	0.78875	0.033
57DAP/reference	0.86378	0.069

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03185	0.712
17DAP/reference	1.0017	0.805
27DAP/reference	1.01372	1
39DAP/reference	1.0134	1
41DAP/reference	0.95363	0.277
42DAP/reference	0.91744	0.108
43DAP/reference	1.01105	1
47DAP/reference	0.92352	0.032
52DAP/reference	0.97431	0.38
57DAP/reference	1.0919	0.108

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12044	0.047
17DAP/reference	0.93348	0.144
27DAP/reference	0.8927	0.044
39DAP/reference	0.91559	0.035
41DAP/reference	0.95005	0.167
42DAP/reference	0.82729	0.025
43DAP/reference	0.8759	0.028
47DAP/reference	0.84718	0.06
52DAP/reference	1.06949	0.714
57DAP/reference	0.94467	0.43

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.92724	1
26DAP/20DAP	0.94625	1
34DAP/26DAP	1.16928	0.542
51DAP/34DAP	1.09879	0.303
52DAP/51DAP	1.06519	0.534
53DAP/52DAP	0.83165	0.19
55DAP/53DAP	0.84131	0.203
57DAP/55DAP	0.90155	0.619
62DAP/57DAP	1.0546	0.868
68DAP/62DAP	0.99008	0.885
68DAP/14DAP	0.87266	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.56212	0.031

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.43707	0.162
Mature Green Tomato/Ripe Tomato	1.97167	0.026
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	4.96992	1
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95904
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	0.67416
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	0.66653
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.89605
6-2/M82	0.87621
6-3/M82	N/A	N/A
7-1/M82	1.23402
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.00631	1
IL2-6/WTpooled	0.74329
IL7-5/WTpooled	1.06377	0.792
IL7-3/WTpooled	1.37762	1
IL12-4/WTpooled	1.13591	0.673
IL1-4/WTpooled	1.17618	1
WT/WTpooled	0.97372	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	0.97796	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08913	0.921
DC3000/delta hrp 6h	0.95726	0.95
DC3000/delta hrp 12h	1.02297	1
DC3000/delta hrp 24h	0.80313	0.037

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.60685	0.023
DC3000 delta B/DC3000 delta AB	0.6209	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.10803	1
Exp 36h	1.03848	1
Exp 60h	1.40491	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00558	1
Var 0h	2.43417	1
Var 12h I row2-row1	0.76039	0.338
Var 12h NI row2-row1	0.99613	1
Var 36h I row2-row1	1.11303	0.908
Var 36h NI row2-row1	1.21546	0.253
Var 60h I row2-row1	0.97697	0.293
Var 60h NI row2-row1	1.18382	0.904
Time course 0hI-0hNI	0.99898	1
Time course 12hI-12hNI	0.99119	0.978
Time course 36hI-36hNI	1.01212	1
Time course 60hI-60hNI	0.23415	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)	1.01973	1
transgenic ySAMdc/azygous control (breaker)	1.03584	1
transgenic ySAMdc/azygous control (red)	1.07204	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02474	0.421

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.99245	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.97938	1
Manapal/WT (break)	1.0515	1
Manapal/WT (red)	1.19066	0.137