Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-3.2.10.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.30182	0.878
27DAP/17DAP	1.1572	0.833
39DAP/27DAP	0.80325	0.462
41DAP/39DAP	1.25512	0.535
42DAP/41DAP	0.90912	0.774
43DAP/42DAP	0.95364	0.867
47DAP/43DAP	1.17586	0.513
52DAP/47DAP	0.83505	0.551
57DAP/52DAP	1.03841	0.918

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95859	0.39
17DAP/reference	0.99767	0.957
27DAP/reference	1.00411	0.885
39DAP/reference	0.89348	0.188
41DAP/reference	0.95707	0.542
42DAP/reference	0.85581	0.022
43DAP/reference	0.98839	0.785
47DAP/reference	0.84507	0.016
52DAP/reference	0.75624	0.036
57DAP/reference	0.85495	0.042

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93042	0.388
27DAP/17DAP	1.02086	0.976
39DAP/27DAP	1.06298	0.512
41DAP/39DAP	1.02592	0.837
42DAP/41DAP	0.95737	0.617
43DAP/42DAP	1.02939	0.554
47DAP/43DAP	0.99948	1
52DAP/47DAP	0.99136	0.941
57DAP/52DAP	0.94393	0.391
57DAP/7DAP	1.05298	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80191	0.086
17DAP/reference	0.92092	0.295
27DAP/reference	1.06994	0.371
39DAP/reference	0.8849	0.17
41DAP/reference	0.83876	0.064
42DAP/reference	0.90565	0.211
43DAP/reference	0.96028	0.403
47DAP/reference	0.80953	0.079
52DAP/reference	0.86362	0.106
57DAP/reference	0.83184	0.061

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01814	0.993
17DAP/reference	1.09919	0.708
27DAP/reference	0.905	0.304
39DAP/reference	0.67573	0.024
41DAP/reference	0.70168	0.017
42DAP/reference	0.8131	0.037
43DAP/reference	0.99892	0.748
47DAP/reference	0.82601	0.013
52DAP/reference	0.7521	0.004
57DAP/reference	0.79466	0.018

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0892	0.456
17DAP/reference	1.09676	0.62
27DAP/reference	0.87578	0.133
39DAP/reference	0.92402	0.36
41DAP/reference	0.88064	0.132
42DAP/reference	0.85815	0.172
43DAP/reference	0.74468	0.036
47DAP/reference	0.69752	0.005
52DAP/reference	0.88161	0.351
57DAP/reference	0.70505	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93766	1
26DAP/20DAP	0.97766	1
34DAP/26DAP	0.98473	0.972
51DAP/34DAP	1.02219	0.936
52DAP/51DAP	1.03351	0.596
53DAP/52DAP	1.02832	0.83
55DAP/53DAP	0.95641	0.604
57DAP/55DAP	1.03834	0.947
62DAP/57DAP	1.02217	1
68DAP/62DAP	0.92137	0.722
68DAP/14DAP	0.9853	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02618	0.558

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.03423	0.068
Mature Green Tomato/Ripe Tomato	0.84392	0.226
Immature Eggplant/Mature Eggplant	2.08853	0.05
Ripe Pepper/Ripe Tomato	19.8713	N/A
Mature Eggplant/Ripe Tomato	0.17592	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.70628	1
12-2/M82	N/A	N/A
12-4/M82	0.73886	0.358
1-3/M82	N/A	N/A
2-1-1/M82	1.29725	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	0.99292	N/A
4-3-2/M82	0.8472	1
4-3/M82	N/A	N/A
5-3/M82	0.73142	0.642
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	2.11205	N/A
9-3-2/M82	0.88427	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.01696	1
IL2-6/WTpooled	1.09923	1
IL7-5/WTpooled	0.94939	1
IL7-3/WTpooled	0.95541	1
IL12-4/WTpooled	0.96308	1
IL1-4/WTpooled	1.05903	1
WT/WTpooled	1.04472	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	1.10625	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06405	0.921
DC3000/delta hrp 6h	0.97119	0.95
DC3000/delta hrp 12h	0.96789	1
DC3000/delta hrp 24h	1.53065	0.099

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.20323	0.06
DC3000 delta B/DC3000 delta AB	1.07133	0.415

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97295	1
Exp 36h	0.99293	1
Exp 60h	0.88506	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95663	1
Var 0h	0.9075	1
Var 12h I row2-row1	1.02883	0.692
Var 12h NI row2-row1	0.90648	0.627
Var 36h I row2-row1	1.05772	0.489
Var 36h NI row2-row1	0.99071	0.852
Var 60h I row2-row1	0.9904	0.832
Var 60h NI row2-row1	1.10832	0.904
Time course 0hI-0hNI	1.06515	0.852
Time course 12hI-12hNI	1.15858	0.046
Time course 36hI-36hNI	1.40415	0.014
Time course 60hI-60hNI	1.7173	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)	1.12664	0.699
transgenic ySAMdc/azygous control (breaker)	2.33323	0.166
transgenic ySAMdc/azygous control (red)	1.09472	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.87533	0.077

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.50624	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	6.78288	0.083
Manapal/WT (break)	3.12816	0.123
Manapal/WT (red)	1.68634	1