Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.9.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97117	0.779
27DAP/17DAP	0.85805	0.67
39DAP/27DAP	1.09424	0.906
41DAP/39DAP	1.16292	0.63
42DAP/41DAP	1.14198	0.841
43DAP/42DAP	1.10319	0.968
47DAP/43DAP	1.10084	0.746
52DAP/47DAP	0.87749	0.637
57DAP/52DAP	0.93822	0.849

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0366	0.846
17DAP/reference	0.79272	0.138
27DAP/reference	0.93833	0.457
39DAP/reference	0.94848	0.487
41DAP/reference	0.82809	0.021
42DAP/reference	1.13457	0.103
43DAP/reference	1.00044	0.924
47DAP/reference	1.22412	0.015
52DAP/reference	0.9238	0.158
57DAP/reference	1.18307	0.091

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98988	0.801
27DAP/17DAP	0.93695	0.144
39DAP/27DAP	0.98647	0.898
41DAP/39DAP	0.95388	0.63
42DAP/41DAP	1.03165	0.947
43DAP/42DAP	0.98078	0.774
47DAP/43DAP	0.98935	0.939
52DAP/47DAP	0.98194	0.901
57DAP/52DAP	0.96307	0.581
57DAP/7DAP	0.97447	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17548	0.088
17DAP/reference	1.04105	0.244
27DAP/reference	1.15157	0.008
39DAP/reference	0.95712	0.198
41DAP/reference	0.88951	0.03
42DAP/reference	0.83143	0.01
43DAP/reference	1.0588	0.241
47DAP/reference	1.09784	0.266
52DAP/reference	1.77891	0.007
57DAP/reference	1.44508	0.024

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91307	0.362
17DAP/reference	0.96585	0.389
27DAP/reference	0.93678	0.366
39DAP/reference	0.99422	0.621
41DAP/reference	0.92523	0.164
42DAP/reference	0.98738	0.655
43DAP/reference	1.10659	0.793
47DAP/reference	1.05504	0.274
52DAP/reference	1.06121	0.702
57DAP/reference	0.93819	0.384

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.36663	0.015
17DAP/reference	0.90282	0.144
27DAP/reference	1.03853	0.392
39DAP/reference	1.46801	0.067
41DAP/reference	1.28104	0.045
42DAP/reference	1.13253	0.251
43DAP/reference	1.0821	0.49
47DAP/reference	1.19339	0.12
52DAP/reference	1.24193	0.095
57DAP/reference	1.2334	0.028

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16384	0.966
26DAP/20DAP	0.90625	0.512
34DAP/26DAP	0.99983	1
51DAP/34DAP	1.12437	0.293
52DAP/51DAP	1.02577	0.708
53DAP/52DAP	0.95013	0.848
55DAP/53DAP	1.04507	0.861
57DAP/55DAP	1.2165	0.274
62DAP/57DAP	0.99136	1
68DAP/62DAP	1.26838	0.635
68DAP/14DAP	3.75825	0.019

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.98809	0.665

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.71081	0.193
Mature Green Tomato/Ripe Tomato	1.2775	0.478
Immature Eggplant/Mature Eggplant	1.02077	0.683
Ripe Pepper/Ripe Tomato	2.14722	0.258
Mature Eggplant/Ripe Tomato	1.41848	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.91126	0.708
1-1-2/M82	1.13384	1
12-2/M82	1.09547	1
12-4/M82	1.03778	1
1-3/M82	1.837	0.248
2-1-1/M82	0.90626
2-1/M82	N/A	N/A
2-6/M82	0.81092	1
3-2/M82	N/A	N/A
4-1-1/M82	0.89932	1
4-1/M82	0.99981	1
4-3-2/M82	0.81189
4-3/M82	0.95643	1
5-3/M82	1.06224	1
6-2/M82	1.11779	1
6-3/M82	0.97021	1
7-1/M82	1.16042	0.592
7-2/M82	1.09209	1
9-3-2/M82	1.17546	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	2.2245	0.277
IL2-6/WTpooled	1.1105	0.531
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.18108	1
IL12-4/WTpooled	1.13408	0.695
IL1-4/WTpooled	3.77224	1
WT/WTpooled	0.95163	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	1.26307	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09685	0.75
DC3000/delta hrp 6h	0.85082	0.95
DC3000/delta hrp 12h	0.81656	1
DC3000/delta hrp 24h	1.29204	0.221

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.06329	0.208
DC3000 delta B/DC3000 delta AB	1.06093	0.453

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94476	1
Exp 36h	0.91135	0.749
Exp 60h	1.14201	1

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	0.95373	0.936
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)	0.89441	0.409
transgenic ySAMdc/azygous control (breaker)	1.12752	1
transgenic ySAMdc/azygous control (red)	0.86746	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.32398	0.057

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.64753	0.172
Manapal/WT (break)	1.12906	1
Manapal/WT (red)	0.92433	0.315