Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.8.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.53141	0.183
27DAP/17DAP	1.86523	0.513
39DAP/27DAP	1.09643	1
41DAP/39DAP	0.69363	0.2
42DAP/41DAP	1.13309	0.971
43DAP/42DAP	0.70912	0.589
47DAP/43DAP	1.06238	0.95
52DAP/47DAP	1.35004	0.991
57DAP/52DAP	1.45061	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	N/A	N/A
17DAP/reference	0.49478
27DAP/reference	1.0858
39DAP/reference	0.81239	0.35
41DAP/reference	1.26611
42DAP/reference	0.95107	0.287
43DAP/reference	N/A	N/A
47DAP/reference	0.3332	0.001
52DAP/reference	0.90343	0.461
57DAP/reference	1.00688	0.58

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9586	0.732
27DAP/17DAP	0.90377	0.537
39DAP/27DAP	1.09631	0.793
41DAP/39DAP	0.91317	0.617
42DAP/41DAP	1.14722	0.308
43DAP/42DAP	1.01618	0.83
47DAP/43DAP	0.98686	0.933
52DAP/47DAP	1.07558	0.776
57DAP/52DAP	1.30601	0.136
57DAP/7DAP	1.30948	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04051	1
17DAP/reference	1.71238	0.017
27DAP/reference	1.83677	0.009
39DAP/reference	0.83097	0.064
41DAP/reference	0.92798	0.326
42DAP/reference	0.6885	0.023
43DAP/reference	0.86546	0.183
47DAP/reference	1.03243	1
52DAP/reference	1.07794	0.941
57DAP/reference	1.16441	0.654

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19247	0.687
17DAP/reference	1.02561	0.873
27DAP/reference	0.73589	0.292
39DAP/reference	1.07477	1
41DAP/reference	0.54881	0.089
42DAP/reference	0.61608	0.067
43DAP/reference	0.79791	0.17
47DAP/reference	0.74128	0.133
52DAP/reference	0.75838	0.093
57DAP/reference	0.59778	0.009

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.68773	0.019
17DAP/reference	1.30073	0.462
27DAP/reference	1.54203	0.025
39DAP/reference	1.50945	0.005
41DAP/reference	1.52452	0.008
42DAP/reference	2.20439	0.006
43DAP/reference	2.26691	0.007
47DAP/reference	0.99496	0.667
52DAP/reference	1.39883	0.341
57DAP/reference	1.55025	0.539

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.85082	1
26DAP/20DAP	0.94657	1
34DAP/26DAP	1.54075	1
51DAP/34DAP	0.95776	0.747
52DAP/51DAP	1.52178	0.288
53DAP/52DAP	1.31619	0.797
55DAP/53DAP	1.09685	0.537
57DAP/55DAP	0.86356	0.427
62DAP/57DAP	1.01383	0.994
68DAP/62DAP	1.27296	0.31
68DAP/14DAP	1.41492	0.594

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.94503	0.443

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	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
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	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
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	N/A	N/A
IL2-6/WTpooled	0.83727	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.89562	0.298
IL12-4/WTpooled	1.02616	1
IL1-4/WTpooled	0.88879	0.562
WT/WTpooled	1.13831	0.957

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	1.18804	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.24851
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.28745
DC3000/delta hrp 24h	0.89283	0.554

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	1.39772	0.315

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	0.94723	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.0806
Var 12h NI row2-row1	0.91085	0.627
Var 36h I row2-row1	0.91041
Var 36h NI row2-row1	1.09104	1
Var 60h I row2-row1	1.00247	1
Var 60h NI row2-row1	0.97909	1
Time course 0hI-0hNI	0.90202	0.297
Time course 12hI-12hNI	0.93552	0.716
Time course 36hI-36hNI	0.90616	0.366
Time course 60hI-60hNI	0.81676	0.015

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)	2.07773	0.862
transgenic ySAMdc/azygous control (breaker)	1.49346	1
transgenic ySAMdc/azygous control (red)	N/A	N/A

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.52609	0.13

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.01266	0.084
Manapal/WT (break)	1.23608	1
Manapal/WT (red)	0.82546	0.424