Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.17.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.78597	0.29
27DAP/17DAP	1.03937	1
39DAP/27DAP	2.32778	0.08
41DAP/39DAP	1.08854	0.941
42DAP/41DAP	1.3625	0.342
43DAP/42DAP	0.8664	0.788
47DAP/43DAP	1.35692	0.584
52DAP/47DAP	0.62834	0.174
57DAP/52DAP	1.11311	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.66285	0.052
17DAP/reference	0.6534	0.007
27DAP/reference	0.75177	0.064
39DAP/reference	0.75571	0.076
41DAP/reference	0.71616	0.01
42DAP/reference	1.27214	0.018
43DAP/reference	1.55216	0.007
47DAP/reference	1.42584	0.002
52DAP/reference	0.83751	0.082
57DAP/reference	1.23119	0.054

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.30165	0.881
27DAP/17DAP	1.5577	0.579
39DAP/27DAP	1.11759	1
41DAP/39DAP	1.09143	1
42DAP/41DAP	0.91231	0.548
43DAP/42DAP	1.25906	0.351
47DAP/43DAP	0.95818	0.886
52DAP/47DAP	1.29369	0.57
57DAP/52DAP	0.7677	0.16
57DAP/7DAP	0.4955

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.653	0.024
17DAP/reference	0.72682	0.012
27DAP/reference	1.0424	0.371
39DAP/reference	0.57766	0.011
41DAP/reference	0.57113	0.015
42DAP/reference	0.77362	0.06
43DAP/reference	0.735	0.02
47DAP/reference	1.05023	1
52DAP/reference	0.78722	0.053
57DAP/reference	0.55467	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.58495	0.198
17DAP/reference	0.85342	0.307
27DAP/reference	0.80272	0.043
39DAP/reference	0.78768	0.122
41DAP/reference	0.75564	0.045
42DAP/reference	0.81196	0.037
43DAP/reference	0.98439	0.539
47DAP/reference	0.96846	0.446
52DAP/reference	0.50318	0.004
57DAP/reference	0.89589	0.298

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.54895	0.022
17DAP/reference	0.75112	0.165
27DAP/reference	0.57935	0.031
39DAP/reference	1.01761	0.889
41DAP/reference	0.75458	0.058
42DAP/reference	1.03739	0.775
43DAP/reference	1.42337	0.229
47DAP/reference	0.98529	0.574
52DAP/reference	0.84418	0.238
57DAP/reference	1.14789	0.66

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.30354	0.966
26DAP/20DAP	0.8894	0.512
34DAP/26DAP	1.52054	0.819
51DAP/34DAP	N/A	N/A
52DAP/51DAP	1.0594	1
53DAP/52DAP	0.97045	0.803
55DAP/53DAP	1.44844	0.075
57DAP/55DAP	1.0246	0.839
62DAP/57DAP	0.95512	0.871
68DAP/62DAP	1.15655	0.539
68DAP/14DAP	1.37166	0.346

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.43427	0.415

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.10516	0.05
Mature Green Tomato/Ripe Tomato	0.50061	0.018
Immature Eggplant/Mature Eggplant	52.6947	0.058
Ripe Pepper/Ripe Tomato	1.47818	1
Mature Eggplant/Ripe Tomato	0.29597	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96889	0.944
1-1-2/M82	1.13511	1
12-2/M82	1.07361	1
12-4/M82	1.84619	1
1-3/M82	3.39647
2-1-1/M82	1.48991	0.179
2-1/M82	N/A	N/A
2-6/M82	1.85382	0.374
3-2/M82	0.9756	1
4-1-1/M82	1.20991
4-1/M82	2.56808	0.853
4-3-2/M82	N/A	N/A
4-3/M82	1.23783
5-3/M82	1.06609	0.572
6-2/M82	1.61112	0.253
6-3/M82	1.09531	1
7-1/M82	0.89633
7-2/M82	1.58012	0.385
9-3-2/M82	2.62678	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.91922	0.247
IL2-6/WTpooled	0.87046	0.473
IL7-5/WTpooled	0.68708	1
IL7-3/WTpooled	1.1044	1
IL12-4/WTpooled	0.9799	1
IL1-4/WTpooled	1.32233	0.426
WT/WTpooled	1.02123	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0441	0.921
DC3000/delta hrp 6h	1.01786	0.95
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	1.51896	0.069

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	1.29331	1
Exp 36h	3.05852	0.371
Exp 60h	2.09799	0.22

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.27036	0.594
Var 12h I row2-row1	1.09871	0.736
Var 12h NI row2-row1	1.06515	1
Var 36h I row2-row1	1.39361
Var 36h NI row2-row1	1.16799
Var 60h I row2-row1	0.86234	0.952
Var 60h NI row2-row1	1.57962	1
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	0.6294
Time course 36hI-36hNI	1.88456	0.008
Time course 60hI-60hNI	7.67337	0.009

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)	1.16594	0.921
transgenic ySAMdc/azygous control (breaker)	1.07653	1
transgenic ySAMdc/azygous control (red)	0.88548	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.42894	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92126	1
Manapal/WT (break)	0.76883	0.299
Manapal/WT (red)	0.97453	0.863