Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-8.3.6.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.41828	0.365
27DAP/17DAP	1.23722	0.793
39DAP/27DAP	1.00253	0.782
41DAP/39DAP	1.38469	0.392
42DAP/41DAP	1.21252	0.691
43DAP/42DAP	0.80807	0.713
47DAP/43DAP	0.87177	0.584
52DAP/47DAP	1.69509	0.258
57DAP/52DAP	0.83739	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30532	0.025
17DAP/reference	0.94006	0.278
27DAP/reference	0.97485	0.623
39DAP/reference	0.98302	0.762
41DAP/reference	1.12575	0.158
42DAP/reference	0.84207	0.014
43DAP/reference	0.95259	0.36
47DAP/reference	0.81994	0.01
52DAP/reference	0.84755	0.075
57DAP/reference	0.99097	0.671

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.44636	0.065
27DAP/17DAP	1.06028	0.751
39DAP/27DAP	1.24509	0.103
41DAP/39DAP	1.16134	0.238
42DAP/41DAP	0.94431	0.576
43DAP/42DAP	1.18496	0.042
47DAP/43DAP	0.94927	0.764
52DAP/47DAP	0.96009	0.848
57DAP/52DAP	1.0502	0.818
57DAP/7DAP	1.4963	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02315	1
17DAP/reference	0.77851	0.014
27DAP/reference	0.85331	0.01
39DAP/reference	0.89752	0.025
41DAP/reference	0.91539	0.098
42DAP/reference	0.89511	0.2
43DAP/reference	0.84743	0.061
47DAP/reference	0.8444	0.222
52DAP/reference	0.88402	0.028
57DAP/reference	0.97128	0.458

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.85231	0.038
17DAP/reference	1.08157	0.484
27DAP/reference	0.89858	0.257
39DAP/reference	0.82551	0.108
41DAP/reference	1.07023	1
42DAP/reference	1.04185	0.951
43DAP/reference	1.39896	0.247
47DAP/reference	1.00826	0.833
52DAP/reference	0.99313	0.761
57DAP/reference	0.98278	0.789

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95357	0.391
17DAP/reference	0.96678	0.615
27DAP/reference	0.90487	0.062
39DAP/reference	0.83825	0.019
41DAP/reference	0.9633	0.331
42DAP/reference	0.81906	0.032
43DAP/reference	0.78373	0.027
47DAP/reference	0.88364	0.207
52DAP/reference	0.71624	0.069
57DAP/reference	0.82011	0.149

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0659	0.966
26DAP/20DAP	0.97718	1
34DAP/26DAP	1.16776	1
51DAP/34DAP	1.47027	0.052
52DAP/51DAP	0.72961	1
53DAP/52DAP	2.09539	0.027
55DAP/53DAP	1.00688	0.951
57DAP/55DAP	0.66418	0.032
62DAP/57DAP	0.98458	0.994
68DAP/62DAP	0.90893	0.769
68DAP/14DAP	0.63137	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.19541	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	7.69596	0.059
Mature Green Tomato/Ripe Tomato	1.0235	1
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.51471	N/A
Mature Eggplant/Ripe Tomato	0.45342	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.79083	N/A
1-1-2/M82	0.64677	N/A
12-2/M82	0.92639	N/A
12-4/M82	0.88939	0.358
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	0.96866	N/A
4-1-1/M82	N/A	N/A
4-1/M82	0.66444	0.998
4-3-2/M82	0.76794	0.698
4-3/M82	0.87575	0.72
5-3/M82	1.01668	1
6-2/M82	1.97448	N/A
6-3/M82	0.79565	N/A
7-1/M82	1.01891	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.69103	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.98439	1
IL2-6/WTpooled	1.05047	1
IL7-5/WTpooled	1.18938	0.792
IL7-3/WTpooled	0.84609	0.31
IL12-4/WTpooled	1.13216	0.503
IL1-4/WTpooled	1.03223	1
WT/WTpooled	0.95665	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	1.23199	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.13496	0.921
DC3000/delta hrp 6h	0.81487	N/A
DC3000/delta hrp 12h	1.12793	1
DC3000/delta hrp 24h	0.82699	0.107

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	1.04139	1
Exp 36h	1.05241	1
Exp 60h	0.94635	0.266

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00766	1
Var 0h	1.14236	0.98
Var 12h I row2-row1	1.0737	0.296
Var 12h NI row2-row1	0.8866	0.82
Var 36h I row2-row1	1.3739	0.368
Var 36h NI row2-row1	1.32879	0.276
Var 60h I row2-row1	0.99518	1
Var 60h NI row2-row1	0.94591	0.977
Time course 0hI-0hNI	1.16692	0.182
Time course 12hI-12hNI	1.04056	0.811
Time course 36hI-36hNI	1.23324	0.089
Time course 60hI-60hNI	1.00079	1

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)	0.70763	0.213
transgenic ySAMdc/azygous control (breaker)	1.15073	1
transgenic ySAMdc/azygous control (red)	0.95466	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01572	0.372

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.9655	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.1292	0.307
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	1.32807	0.413