Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.15.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.43554	0.014
27DAP/17DAP	1.02999	0.817
39DAP/27DAP	1.17786	1
41DAP/39DAP	1.4468	0.293
42DAP/41DAP	0.93741	1
43DAP/42DAP	0.67386	0.497
47DAP/43DAP	1.21457	0.444
52DAP/47DAP	1.45822	0.804
57DAP/52DAP	1.16726	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23241	0.049
17DAP/reference	0.99011	0.819
27DAP/reference	1.01317	0.934
39DAP/reference	0.91767	0.24
41DAP/reference	0.92821	0.114
42DAP/reference	0.80963	0.001
43DAP/reference	0.96866	0.594
47DAP/reference	0.8255	0.003
52DAP/reference	0.8665	0.024
57DAP/reference	0.86272	0.031

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.64571	0.116
27DAP/17DAP	1.1252	0.794
39DAP/27DAP	0.99603	0.908
41DAP/39DAP	0.84886	0.104
42DAP/41DAP	1.13911	0.495
43DAP/42DAP	1.09454	0.699
47DAP/43DAP	0.97987	0.923
52DAP/47DAP	1.16234	0.527
57DAP/52DAP	0.97848	0.773
57DAP/7DAP	0.60407	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.386	0.058
17DAP/reference	1.45885	0.006
27DAP/reference	1.32894	0.03
39DAP/reference	1.49545	0.007
41DAP/reference	1.54973	0.016
42DAP/reference	1.42895	0.006
43DAP/reference	1.60516	0.007
47DAP/reference	1.05728	1
52DAP/reference	1.35896	0.008
57DAP/reference	1.39284	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87515	0.1
17DAP/reference	0.73199	0.006
27DAP/reference	0.87084	0.115
39DAP/reference	0.77515	0.01
41DAP/reference	0.87285	0.023
42DAP/reference	0.88619	0.061
43DAP/reference	0.71598	0.011
47DAP/reference	0.78404	0.01
52DAP/reference	0.75425	0.004
57DAP/reference	0.71349	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30971	0.035
17DAP/reference	1.05833	0.865
27DAP/reference	1.50423	0.035
39DAP/reference	1.30387	0.039
41DAP/reference	1.36821	0.035
42DAP/reference	1.15421	0.294
43DAP/reference	1.17925	0.505
47DAP/reference	0.82837	0.008
52DAP/reference	1.13581	0.837
57DAP/reference	0.95344	0.424

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1142	0.966
26DAP/20DAP	0.91437	1
34DAP/26DAP	1.20276	1
51DAP/34DAP	1.08807	0.814
52DAP/51DAP	1.15706	0.596
53DAP/52DAP	0.91956	0.631
55DAP/53DAP	1.13918	0.782
57DAP/55DAP	1.08338	0.969
62DAP/57DAP	1.16512	0.622
68DAP/62DAP	1.26451	0.565
68DAP/14DAP	0.97855	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.82157	0.322

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.16512	0.078
Ripe Pepper/Ripe Tomato	0.48888	1
Mature Eggplant/Ripe Tomato	1.92875	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.70612
12-2/M82	1.52306
12-4/M82	0.74187	0.619
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	0.72759	0.395
6-2/M82	0.78855	0.497
6-3/M82	N/A	N/A
7-1/M82	0.80265
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	1.04271	0.493
IL2-6/WTpooled	0.75079	0.383
IL7-5/WTpooled	0.95078	1
IL7-3/WTpooled	0.96277	1
IL12-4/WTpooled	1.11989	0.624
IL1-4/WTpooled	0.91422	0.834
WT/WTpooled	1.09568	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	1.59541	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93559	1
DC3000/delta hrp 6h	1.14231	0.857
DC3000/delta hrp 12h	0.85673	1
DC3000/delta hrp 24h	4.2701	0.018

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.37487	0.063
DC3000 delta B/DC3000 delta AB	1.26054	0.479

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.93469	0.623
Exp 60h	1.06623	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05061	1
Var 0h	1.16401	0.782
Var 12h I row2-row1	1.11967	0.235
Var 12h NI row2-row1	0.7691	0.546
Var 36h I row2-row1	1.21466	0.601
Var 36h NI row2-row1	0.96942	0.852
Var 60h I row2-row1	0.99571	1
Var 60h NI row2-row1	1.51054	0.904
Time course 0hI-0hNI	1.14805	0.799
Time course 12hI-12hNI	1.11181	0.615
Time course 36hI-36hNI	1.2481	0.039
Time course 60hI-60hNI	1.47066	0.008

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)	0.94329	0.614
transgenic ySAMdc/azygous control (breaker)	1.05408	1
transgenic ySAMdc/azygous control (red)	1.20966	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.29726	0.059

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.76458	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.54273	1
Manapal/WT (break)	0.89802	1
Manapal/WT (red)	0.7865	0.315