Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.10.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07961	0.932
27DAP/17DAP	0.97153	0.978
39DAP/27DAP	1.06157	0.972
41DAP/39DAP	1.03122	1
42DAP/41DAP	0.93466	1
43DAP/42DAP	1.1546	0.875
47DAP/43DAP	1.09624	0.442
52DAP/47DAP	0.96267	0.786
57DAP/52DAP	1.09992	0.948

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68495	0.027
17DAP/reference	0.60658	0.013
27DAP/reference	0.77068	0.023
39DAP/reference	0.69037	0.029
41DAP/reference	0.58673	0.021
42DAP/reference	0.82635	0.02
43DAP/reference	0.78052	0.015
47DAP/reference	0.87289	0.071
52DAP/reference	1.15236	0.195
57DAP/reference	1.02706	0.802

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85667	0.238
27DAP/17DAP	1.07347	0.826
39DAP/27DAP	0.98484	0.887
41DAP/39DAP	0.89874	0.481
42DAP/41DAP	1.11708	0.984
43DAP/42DAP	1.05313	0.554
47DAP/43DAP	1.03228	0.934
52DAP/47DAP	1.10382	0.724
57DAP/52DAP	0.95752	0.646
57DAP/7DAP	0.85486	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.72056	0.066
17DAP/reference	0.7041	0.011
27DAP/reference	0.75057	0.01
39DAP/reference	0.8838	0.146
41DAP/reference	0.75123	0.015
42DAP/reference	0.68457	0.01
43DAP/reference	0.79687	0.079
47DAP/reference	0.83571	0.128
52DAP/reference	0.55959	0.011
57DAP/reference	0.84714	0.118

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.60933	0.014
17DAP/reference	0.48064	0.003
27DAP/reference	0.93547	0.366
39DAP/reference	0.94045	0.37
41DAP/reference	1.04708	1
42DAP/reference	0.96565	0.392
43DAP/reference	0.72184	0.108
47DAP/reference	0.66639	0.01
52DAP/reference	0.91635	0.203
57DAP/reference	0.50576	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77513	0.061
17DAP/reference	0.82173	0.224
27DAP/reference	0.92512	0.195
39DAP/reference	0.7806	0.013
41DAP/reference	0.877	0.035
42DAP/reference	0.92627	0.445
43DAP/reference	0.93106	0.384
47DAP/reference	0.85831	0.199
52DAP/reference	0.68964	0.047
57DAP/reference	1.50198	0.059

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03651	1
26DAP/20DAP	1.08888	0.727
34DAP/26DAP	1.14612	1
51DAP/34DAP	0.75302	0.107
52DAP/51DAP	1.17875	0.083
53DAP/52DAP	0.97727	0.848
55DAP/53DAP	1.77804	0.063
57DAP/55DAP	0.74356	0.145
62DAP/57DAP	1.24792	0.569
68DAP/62DAP	4.61682	0.107
68DAP/14DAP	6.00581	0.016

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.92669	0.253

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.70038	0.021
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.89673
Mature Eggplant/Ripe Tomato	1.41554

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98621
1-1-2/M82	0.85239
12-2/M82	N/A	N/A
12-4/M82	0.91456	1
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	1.02556	1
4-1-1/M82	N/A	N/A
4-1/M82	0.9549	1
4-3-2/M82	1.03668	1
4-3/M82	0.91903
5-3/M82	1.01553	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.15312
7-2/M82	1.17234
9-3-2/M82	0.99343	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.895	1
IL7-5/WTpooled	0.82244
IL7-3/WTpooled	0.8461	0.418
IL12-4/WTpooled	1.01386	0.839
IL1-4/WTpooled	1.1078	1
WT/WTpooled	1.11593	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	1.11862	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.8987	1
DC3000/delta hrp 6h	1.33907	1
DC3000/delta hrp 12h	1.11315	1
DC3000/delta hrp 24h	0.81075	0.17

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.01461	1
DC3000 delta B/DC3000 delta AB	0.93452	0.511

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98346	1
Exp 36h	0.88	0.699
Exp 60h	0.83478	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96809	1
Var 0h	1.09047	1
Var 12h I row2-row1	1.08648	0.406
Var 12h NI row2-row1	1.13997	1
Var 36h I row2-row1	1.0152	1
Var 36h NI row2-row1	1.08638	1
Var 60h I row2-row1	0.9835	0.952
Var 60h NI row2-row1	1.03225	1
Time course 0hI-0hNI	0.94229	0.522
Time course 12hI-12hNI	0.9688	0.746
Time course 36hI-36hNI	0.86141	0.042
Time course 60hI-60hNI	0.54538	0.006

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)	1.05819	0.541
transgenic ySAMdc/azygous control (breaker)	1.19863	0.248
transgenic ySAMdc/azygous control (red)	1.04908	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9297	0.059

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.83758	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.98949	1
Manapal/WT (break)	0.96979	1
Manapal/WT (red)	1.30004	0.222