Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.15.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90973	0.532
27DAP/17DAP	1.01802	0.99
39DAP/27DAP	0.82256	0.443
41DAP/39DAP	1.44519	0.367
42DAP/41DAP	1.03611	1
43DAP/42DAP	0.87507	0.695
47DAP/43DAP	0.90675	0.687
52DAP/47DAP	1.34695	0.406
57DAP/52DAP	0.89025	0.85

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29011	0.022
17DAP/reference	1.15516	0.014
27DAP/reference	1.08776	0.165
39DAP/reference	1.16648	0.038
41DAP/reference	1.31043	0.026
42DAP/reference	1.33817	0.001
43DAP/reference	1.03781	0.812
47DAP/reference	1.12066	0.003
52DAP/reference	1.20879	0.015
57DAP/reference	1.05196	0.829

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01345	0.858
27DAP/17DAP	1.02359	0.912
39DAP/27DAP	1.04241	0.626
41DAP/39DAP	0.93743	0.63
42DAP/41DAP	1.03278	0.727
43DAP/42DAP	1.00979	0.746
47DAP/43DAP	1.03288	0.837
52DAP/47DAP	1.0049	0.991
57DAP/52DAP	1.00487	1
57DAP/7DAP	1.15321	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01427	1
17DAP/reference	0.91823	0.082
27DAP/reference	0.93989	0.039
39DAP/reference	1.01956	0.436
41DAP/reference	1.07597	0.113
42DAP/reference	1.00153	1
43DAP/reference	0.96866	0.145
47DAP/reference	0.91005	0.222
52DAP/reference	1.0497	0.526
57DAP/reference	0.93603	0.059

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24165	0.097
17DAP/reference	1.31083	0.046
27DAP/reference	1.26801	0.093
39DAP/reference	1.32536	0.065
41DAP/reference	1.3727	0.011
42DAP/reference	1.29235	0.03
43DAP/reference	1.15463	0.205
47DAP/reference	1.30466	0.009
52DAP/reference	1.2245	0.007
57DAP/reference	1.31286	0.014

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08098	0.758
17DAP/reference	1.15282	0.243
27DAP/reference	1.01519	1
39DAP/reference	0.96336	0.246
41DAP/reference	0.94252	0.331
42DAP/reference	0.95154	0.552
43DAP/reference	1.20043	0.302
47DAP/reference	1.19648	0.044
52DAP/reference	0.85473	0.174
57DAP/reference	1.03953	0.867

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.13856	0.966
26DAP/20DAP	0.99831	1
34DAP/26DAP	0.95681	0.857
51DAP/34DAP	0.93897	0.537
52DAP/51DAP	0.9823	1
53DAP/52DAP	1.08904	0.307
55DAP/53DAP	1.07966	0.981
57DAP/55DAP	1.00734	0.938
62DAP/57DAP	1.00748	0.994
68DAP/62DAP	0.91271	0.668
68DAP/14DAP	0.69895	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.91076	0.102

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.09886	0.176
Mature Green Tomato/Ripe Tomato	0.74815	0.026
Immature Eggplant/Mature Eggplant	0.58373	0.084
Ripe Pepper/Ripe Tomato	1.8111
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02015	1
1-1-2/M82	0.9406	1
12-2/M82	1.18249	1
12-4/M82	1.03205	1
1-3/M82	1.05224	1
2-1-1/M82	1.1585
2-1/M82	N/A	N/A
2-6/M82	1.02769	0.395
3-2/M82	0.92569	1
4-1-1/M82	1.28796	0.872
4-1/M82	0.73561	0.867
4-3-2/M82	0.6145
4-3/M82	1.28375	0.268
5-3/M82	1.03522	1
6-2/M82	0.97734	1
6-3/M82	0.94939	1
7-1/M82	0.68501
7-2/M82	1.07613	1
9-3-2/M82	0.74487	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.66646	0.243
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.54677	1
IL7-3/WTpooled	0.97269	1
IL12-4/WTpooled	0.96383	1
IL1-4/WTpooled	1.81797	1
WT/WTpooled	0.90197	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	0.968	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9796	1
DC3000/delta hrp 6h	0.98719	0.95
DC3000/delta hrp 12h	1.09825	1
DC3000/delta hrp 24h	0.96396	0.75

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.9532	0.568
DC3000 delta B/DC3000 delta AB	0.97136	0.674

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.08025	1
Exp 36h	0.64016	0.623
Exp 60h	0.62714	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9737	1
Var 0h	0.87876	0.933
Var 12h I row2-row1	1.02634	0.654
Var 12h NI row2-row1	1.01014	1
Var 36h I row2-row1	0.9163	1
Var 36h NI row2-row1	1.40507	1
Var 60h I row2-row1	1.3142	0.562
Var 60h NI row2-row1	1.07842	0.904
Time course 0hI-0hNI	1.05309	0.799
Time course 12hI-12hNI	1.01368	0.868
Time course 36hI-36hNI	0.95019	0.317
Time course 60hI-60hNI	0.95757	0.646

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)	1.13189	0.318
transgenic ySAMdc/azygous control (breaker)	1.10401	1
transgenic ySAMdc/azygous control (red)	1.32756	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.91936	0.048

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.64584	0.228

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.90814	0.096
Manapal/WT (break)	2.50374	0.13
Manapal/WT (red)	1.18087	1