Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.20.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.78479	0.522
27DAP/17DAP	1.53731	0.725
39DAP/27DAP	1.65047	0.32
41DAP/39DAP	1.16269	0.292
42DAP/41DAP	0.93534	1
43DAP/42DAP	1.44384	0.538
47DAP/43DAP	0.85831	0.48
52DAP/47DAP	1.68304	0.879
57DAP/52DAP	1.07475	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84698	0.029
17DAP/reference	0.98491	0.737
27DAP/reference	1.04535	0.587
39DAP/reference	1.00389	0.991
41DAP/reference	0.994	0.814
42DAP/reference	0.85266	0.008
43DAP/reference	0.93508	0.429
47DAP/reference	0.84886	0.014
52DAP/reference	0.79096	0.014
57DAP/reference	1.0152	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.86088	0.058
27DAP/17DAP	1.08867	0.945
39DAP/27DAP	0.9609	0.732
41DAP/39DAP	1.22862	0.807
42DAP/41DAP	0.80405	0.208
43DAP/42DAP	0.93622	0.576
47DAP/43DAP	1.01727	0.954
52DAP/47DAP	0.99578	0.947
57DAP/52DAP	1.09682	0.875
57DAP/7DAP	0.75642	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96535	0.296
17DAP/reference	0.99246	0.599
27DAP/reference	0.86076	0.037
39DAP/reference	0.82589	0.02
41DAP/reference	0.9148	0.259
42DAP/reference	0.85535	0.055
43DAP/reference	0.95377	0.351
47DAP/reference	0.90214	0.128
52DAP/reference	0.94863	0.304
57DAP/reference	0.84529	0.021

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78693	0.031
17DAP/reference	0.75958	0.021
27DAP/reference	0.82065	0.022
39DAP/reference	0.85973	0.067
41DAP/reference	1.01475	1
42DAP/reference	0.91794	0.135
43DAP/reference	0.88718	0.186
47DAP/reference	0.86934	0.043
52DAP/reference	0.9653	0.433
57DAP/reference	0.8064	0.046

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98941	0.653
17DAP/reference	0.93541	0.198
27DAP/reference	0.97967	0.594
39DAP/reference	1.05021	0.466
41DAP/reference	0.94092	0.264
42DAP/reference	0.87662	0.087
43DAP/reference	0.95047	0.449
47DAP/reference	0.96272	0.434
52DAP/reference	1.10544	0.941
57DAP/reference	1.48988	0.694

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.17334	0.966
26DAP/20DAP	0.89556	1
34DAP/26DAP	1.03221	1
51DAP/34DAP	1.57227	0.677
52DAP/51DAP	1.00147	1
53DAP/52DAP	0.60153	0.102
55DAP/53DAP	1.07812	0.981
57DAP/55DAP	1.23989	0.94
62DAP/57DAP	0.98199	0.994
68DAP/62DAP	1.26078	0.872
68DAP/14DAP	1.05657	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.23625	0.627

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	N/A	N/A
Ripe Pepper/Ripe Tomato	1.03568
Mature Eggplant/Ripe Tomato	0.35115

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00679	1
1-1-2/M82	0.90746	1
12-2/M82	1.08027	1
12-4/M82	1.03326
1-3/M82	0.63103
2-1-1/M82	0.99676
2-1/M82	N/A	N/A
2-6/M82	1.09258	0.329
3-2/M82	0.95754
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	0.66905	0.292
5-3/M82	0.97924	1
6-2/M82	0.8515
6-3/M82	1.1433
7-1/M82	0.96269
7-2/M82	0.72117	0.599
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.76781	0.247
IL2-6/WTpooled	1.15092	1
IL7-5/WTpooled	1.19764	0.792
IL7-3/WTpooled	1.12025	1
IL12-4/WTpooled	1.03279	0.891
IL1-4/WTpooled	0.90874	0.699
WT/WTpooled	1.05486	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	0.84138

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91651	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.86792
DC3000/delta hrp 24h	1.09152	0.411

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

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

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

hybridization	ratio	FDR (corrected p value)
self-self	1.13999	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.4648	0.58
Var 12h NI row2-row1	1.03744	1
Var 36h I row2-row1	1.30435	0.368
Var 36h NI row2-row1	0.54552	1
Var 60h I row2-row1	1.05145	1
Var 60h NI row2-row1	0.49355	0.977
Time course 0hI-0hNI	1.14806	0.867
Time course 12hI-12hNI	1.43816	0.682
Time course 36hI-36hNI	1.24899	0.453
Time course 60hI-60hNI	2.62162	0.022

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)	1.0694	0.571
transgenic ySAMdc/azygous control (breaker)	1.12304	0.248
transgenic ySAMdc/azygous control (red)	0.92366	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08599	0.125

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.81805	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.87241	1
Manapal/WT (break)	1.00798	1
Manapal/WT (red)	0.78473	0.424