Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.12.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16417	0.63
27DAP/17DAP	0.73314	0.22
39DAP/27DAP	1.3411	0.463
41DAP/39DAP	0.50256	0.041
42DAP/41DAP	0.61332	0.774
43DAP/42DAP	0.56642	0.454
47DAP/43DAP	0.28842	0.041
52DAP/47DAP	1.52807	0.327
57DAP/52DAP	1.15142	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.80629	0.006
17DAP/reference	1.55148	0.369
27DAP/reference	0.63948	0.015
39DAP/reference	0.63162	0.013
41DAP/reference	0.83616	0.049
42DAP/reference	0.86541	0.011
43DAP/reference	0.53619	0.015
47DAP/reference	0.54235	0.001
52DAP/reference	0.54811	0.028
57DAP/reference	0.75688	0.01

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.98857	0.038
27DAP/17DAP	1.03057	0.969
39DAP/27DAP	0.37069	0.029
41DAP/39DAP	1.6584	0.603
42DAP/41DAP	0.83222	0.179
43DAP/42DAP	0.66949	0.028
47DAP/43DAP	0.87506	0.347
52DAP/47DAP	1.12415	0.734
57DAP/52DAP	1.3979	0.199
57DAP/7DAP	0.42512	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2439	0.747
17DAP/reference	0.93807	0.082
27DAP/reference	0.94527	0.066
39DAP/reference	0.84755	0.011
41DAP/reference	0.99391	0.589
42DAP/reference	0.81746	0.013
43DAP/reference	0.86492	0.031
47DAP/reference	1.47982	0.331
52DAP/reference	0.84834	0.053
57DAP/reference	0.85004	0.039

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.75005	0.051
17DAP/reference	3.30103	0.007
27DAP/reference	1.9637	0.02
39DAP/reference	2.15801	0.011
41DAP/reference	2.12344	0.005
42DAP/reference	2.45956	0.007
43DAP/reference	1.13005	0.892
47DAP/reference	1.84843	0.008
52DAP/reference	1.63141	0.006
57DAP/reference	0.86092	0.18

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05148	1
17DAP/reference	1.2658	0.333
27DAP/reference	0.94401	0.397
39DAP/reference	0.95007	0.393
41DAP/reference	0.9202	0.167
42DAP/reference	0.89394	0.087
43DAP/reference	0.80367	0.061
47DAP/reference	0.39156	0.004
52DAP/reference	1.27132	0.838
57DAP/reference	0.59589	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16886	0.966
26DAP/20DAP	5.85929	0.097
34DAP/26DAP	0.64441	0.15
51DAP/34DAP	1.29052	0.339
52DAP/51DAP	1.06195	0.708
53DAP/52DAP	1.26703	0.047
55DAP/53DAP	0.75594	0.028
57DAP/55DAP	1.22554	0.841
62DAP/57DAP	0.59307	0.002
68DAP/62DAP	1.01677	1
68DAP/14DAP	0.94481	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.12552	0.591

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.12657	0.058
Mature Green Tomato/Ripe Tomato	5.11907	0.016
Immature Eggplant/Mature Eggplant	1.16682	0.101
Ripe Pepper/Ripe Tomato	1.37118	1
Mature Eggplant/Ripe Tomato	6.44021	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.29944
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	N/A	N/A
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	N/A	N/A
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	1.69229
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.29514
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	1.20733	0.365
IL2-6/WTpooled	0.97692	1
IL7-5/WTpooled	0.93419	1
IL7-3/WTpooled	1.32537	1
IL12-4/WTpooled	1.19653	0.557
IL1-4/WTpooled	1.07517	1
WT/WTpooled	0.95748	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	0.76203	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.15783	0.914
DC3000/delta hrp 6h	0.92947	0.95
DC3000/delta hrp 12h	1.13428	1
DC3000/delta hrp 24h	0.97951	0.91

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.78043	0.031
DC3000 delta B/DC3000 delta AB	0.79429	0.045

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.80025	1
Exp 36h	1.32228	1
Exp 60h	1.00132	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04556	1
Var 0h	0.55808	0.936
Var 12h I row2-row1	1.1923	0.613
Var 12h NI row2-row1	1.06043	1
Var 36h I row2-row1	1.00621	1
Var 36h NI row2-row1	1.07654	1
Var 60h I row2-row1	0.72846	0.439
Var 60h NI row2-row1	1.06409	0.904
Time course 0hI-0hNI	0.92194	0.54
Time course 12hI-12hNI	1.06452	0.73
Time course 36hI-36hNI	0.79939	0.062
Time course 60hI-60hNI	0.6406	0.007

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)	0.95096	0.567
transgenic ySAMdc/azygous control (breaker)	0.33748	0.118
transgenic ySAMdc/azygous control (red)	1.18318	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.17457	0.261

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.35943	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.2919	0.307
Manapal/WT (break)	1.27162	1
Manapal/WT (red)	2.19932	0.15