Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.17.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02504	0.947
27DAP/17DAP	1.09215	1
39DAP/27DAP	1.32737	0.4
41DAP/39DAP	1.12873	0.612
42DAP/41DAP	1.19611	0.882
43DAP/42DAP	1.16952	1
47DAP/43DAP	1.17282	0.856
52DAP/47DAP	1.06611	0.953
57DAP/52DAP	1.3195	0.77

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94134	0.177
17DAP/reference	1.02834	0.631
27DAP/reference	1.10009	0.098
39DAP/reference	0.86305	0.381
41DAP/reference	0.99038	0.814
42DAP/reference	1.00664	1
43DAP/reference	0.97937	0.653
47DAP/reference	0.97778	0.345
52DAP/reference	0.9741	0.546
57DAP/reference	0.96414	0.21

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03107	0.719
27DAP/17DAP	0.99782	0.969
39DAP/27DAP	0.98822	0.932
41DAP/39DAP	1.04862	0.807
42DAP/41DAP	0.99717	0.872
43DAP/42DAP	0.99019	0.96
47DAP/43DAP	0.98909	0.947
52DAP/47DAP	1.05726	0.8
57DAP/52DAP	0.9696	0.622
57DAP/7DAP	1.00817	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92656	0.296
17DAP/reference	0.84982	0.056
27DAP/reference	0.74525	0.011
39DAP/reference	0.85809	0.025
41DAP/reference	0.87053	0.027
42DAP/reference	0.84253	0.015
43DAP/reference	0.76114	0.01
47DAP/reference	1.0132	1
52DAP/reference	0.78404	0.019
57DAP/reference	0.80296	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08717	0.3
17DAP/reference	1.08317	0.151
27DAP/reference	0.95845	0.393
39DAP/reference	1.02896	0.868
41DAP/reference	0.99524	0.631
42DAP/reference	0.92818	0.108
43DAP/reference	0.98519	0.67
47DAP/reference	0.9715	0.39
52DAP/reference	0.99885	0.761
57DAP/reference	0.99955	0.834

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87627	0.127
17DAP/reference	0.93214	0.308
27DAP/reference	0.88871	0.044
39DAP/reference	0.79009	0.022
41DAP/reference	0.89812	0.07
42DAP/reference	0.85092	0.22
43DAP/reference	0.83601	0.024
47DAP/reference	0.88735	0.007
52DAP/reference	0.73256	0.204
57DAP/reference	0.77004	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93548	1
26DAP/20DAP	0.9448	0.512
34DAP/26DAP	0.994	1
51DAP/34DAP	1.07566	0.416
52DAP/51DAP	1.08106	0.261
53DAP/52DAP	0.99125	0.917
55DAP/53DAP	0.90274	0.489
57DAP/55DAP	1.10083	0.881
62DAP/57DAP	0.99543	1
68DAP/62DAP	1.08618	1
68DAP/14DAP	0.963	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.91303	0.137

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.3984	0.078
Mature Green Tomato/Ripe Tomato	1.09693	0.898
Immature Eggplant/Mature Eggplant	1.75523	0.05
Ripe Pepper/Ripe Tomato	2.08279	1
Mature Eggplant/Ripe Tomato	0.71454	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.29786	0.574
1-1-2/M82	1.10497	1
12-2/M82	0.95751	0.862
12-4/M82	1.14735	1
1-3/M82	0.99115	1
2-1-1/M82	1.14338	0.764
2-1/M82	1.51615	1
2-6/M82	1.15166	0.405
3-2/M82	1.14557
4-1-1/M82	1.16833	1
4-1/M82	0.87471
4-3-2/M82	1.33034
4-3/M82	1.3953	0.268
5-3/M82	0.97378	1
6-2/M82	1.26156	0.253
6-3/M82	0.93718	1
7-1/M82	0.97438
7-2/M82	1.27696	0.385
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.06364
IL2-6/WTpooled	1.49709	0.419
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.95674	1
IL12-4/WTpooled	1.1008	0.839
IL1-4/WTpooled	1.38773	1
WT/WTpooled	0.92345	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	1.47674	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91046	1
DC3000/delta hrp 6h	1.02081	1
DC3000/delta hrp 12h	0.9902	1
DC3000/delta hrp 24h	1.12156	0.165

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.03063	0.515
DC3000 delta B/DC3000 delta AB	1.03043	0.609

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98054	1
Exp 36h	1.12585	0.693
Exp 60h	1.06582	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95929	1
Var 0h	1.33655	0.421
Var 12h I row2-row1	1.104	0.272
Var 12h NI row2-row1	1.08569	1
Var 36h I row2-row1	0.91977	1
Var 36h NI row2-row1	0.88361	0.706
Var 60h I row2-row1	1.19651	0.562
Var 60h NI row2-row1	0.99141	1
Time course 0hI-0hNI	1.01577	1
Time course 12hI-12hNI	1.00678	0.888
Time course 36hI-36hNI	1.04338	0.453
Time course 60hI-60hNI	1.43187	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)	1.06443	0.312
transgenic ySAMdc/azygous control (breaker)	1.07199	0.248
transgenic ySAMdc/azygous control (red)	1.0573	0.92

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	0.92638	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.18325	0.083
Manapal/WT (break)	1.07684	1
Manapal/WT (red)	0.88636	0.36