Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.1.17.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16863	0.725
27DAP/17DAP	1.00537	1
39DAP/27DAP	0.99178	0.769
41DAP/39DAP	1.22581	0.464
42DAP/41DAP	1.25494	0.797
43DAP/42DAP	1.17846	0.607
47DAP/43DAP	1.23254	0.4
52DAP/47DAP	1.01567	0.889
57DAP/52DAP	1.12205	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9546	0.371
17DAP/reference	1.05927	0.154
27DAP/reference	0.99295	0.741
39DAP/reference	1.01203	0.828
41DAP/reference	0.99829	1
42DAP/reference	0.96218	0.067
43DAP/reference	1.01351	0.838
47DAP/reference	0.97612	0.224
52DAP/reference	0.95943	0.427
57DAP/reference	0.84922	0.03

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9774	0.663
27DAP/17DAP	0.98493	0.878
39DAP/27DAP	1.05005	0.532
41DAP/39DAP	1.03653	0.748
42DAP/41DAP	0.94991	0.491
43DAP/42DAP	1.01412	0.585
47DAP/43DAP	1.00219	0.973
52DAP/47DAP	1.00446	0.991
57DAP/52DAP	0.9743	0.66
57DAP/7DAP	0.99745	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80428	0.08
17DAP/reference	0.8962	0.192
27DAP/reference	0.84319	0.042
39DAP/reference	0.93164	0.109
41DAP/reference	0.87843	0.122
42DAP/reference	0.8227	0.053
43DAP/reference	0.78725	0.051
47DAP/reference	0.85253	0.168
52DAP/reference	0.91797	0.213
57DAP/reference	0.81745	0.042

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96933	0.623
17DAP/reference	0.91837	0.102
27DAP/reference	0.85281	0.084
39DAP/reference	0.96224	0.281
41DAP/reference	0.90207	0.049
42DAP/reference	0.92833	0.098
43DAP/reference	0.93969	0.307
47DAP/reference	0.96228	0.113
52DAP/reference	0.99716	0.666
57DAP/reference	0.99797	0.834

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84884	0.098
17DAP/reference	0.91191	0.433
27DAP/reference	0.81776	0.081
39DAP/reference	0.82359	0.069
41DAP/reference	0.9411	0.512
42DAP/reference	0.83374	0.172
43DAP/reference	0.95818	0.568
47DAP/reference	0.94346	0.306
52DAP/reference	0.83024	0.15
57DAP/reference	0.69775	0.024

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0122	1
26DAP/20DAP	0.9697	1
34DAP/26DAP	1.01368	1
51DAP/34DAP	1.01811	0.814
52DAP/51DAP	0.97118	1
53DAP/52DAP	1.06848	0.47
55DAP/53DAP	0.96928	0.675
57DAP/55DAP	0.98209	0.904
62DAP/57DAP	0.9499	0.681
68DAP/62DAP	1.20752	0.831
68DAP/14DAP	1.0006	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.95509	0.253

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.46701	0.085
Mature Green Tomato/Ripe Tomato	0.73612
Immature Eggplant/Mature Eggplant	1.55587	0.05
Ripe Pepper/Ripe Tomato	1.38239	1
Mature Eggplant/Ripe Tomato	1.08889	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99794	1
1-1-2/M82	1.03312	1
12-2/M82	0.96468	0.955
12-4/M82	0.98179	0.619
1-3/M82	0.93507	0.378
2-1-1/M82	0.98539	1
2-1/M82	1.29739	1
2-6/M82	1.01136	0.695
3-2/M82	0.96296
4-1-1/M82	1.00301	1
4-1/M82	0.99212
4-3-2/M82	0.82364
4-3/M82	0.9926	1
5-3/M82	1.00466	1
6-2/M82	0.96245	1
6-3/M82	1.00824	1
7-1/M82	1.02392	1
7-2/M82	0.98359	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.87312	0.321
IL2-6/WTpooled	0.9243	1
IL7-5/WTpooled	1.00784	1
IL7-3/WTpooled	0.93766	1
IL12-4/WTpooled	1.0077	1
IL1-4/WTpooled	1.10657	1
WT/WTpooled	0.92341	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	0.86129	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05556	0.921
DC3000/delta hrp 6h	1.08287	0.95
DC3000/delta hrp 12h	1.11154	1
DC3000/delta hrp 24h	1.04766	0.467

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.13695	0.057
DC3000 delta B/DC3000 delta AB	1.14042	0.284

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01272	1
Exp 36h	1.13243	1
Exp 60h	1.14801	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0269	1
Var 0h	1.20502	0.782
Var 12h I row2-row1	1.13834	0.216
Var 12h NI row2-row1	1.00845	1
Var 36h I row2-row1	0.98282	1
Var 36h NI row2-row1	0.92108	0.61
Var 60h I row2-row1	1.2512	0.562
Var 60h NI row2-row1	1.25001	0.904
Time course 0hI-0hNI	0.99778	1
Time course 12hI-12hNI	1.03233	0.788
Time course 36hI-36hNI	0.97604	0.504
Time course 60hI-60hNI	1.32064	0.019

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)	1.15809	0.511
transgenic ySAMdc/azygous control (breaker)	0.8226	0.15
transgenic ySAMdc/azygous control (red)	1.00305	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06071	0.395

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.83614	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.8934	1
Manapal/WT (break)	0.76156	0.333
Manapal/WT (red)	0.85223	0.216