Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.9.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.61484	0.028
27DAP/17DAP	1.25915	0.772
39DAP/27DAP	1.68538	0.159
41DAP/39DAP	0.71496	0.141
42DAP/41DAP	1.00984	1
43DAP/42DAP	0.99577	0.937
47DAP/43DAP	1.10193	0.563
52DAP/47DAP	0.82007	0.54
57DAP/52DAP	1.05345	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17172	0.265
17DAP/reference	0.7961	0.028
27DAP/reference	1.03388	0.966
39DAP/reference	0.97943	0.72
41DAP/reference	0.88771	0.201
42DAP/reference	1.28653	0.001
43DAP/reference	1.09835	0.189
47DAP/reference	1.49834	0.001
52DAP/reference	1.13966	0.083
57DAP/reference	1.33503	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04859	1
27DAP/17DAP	1.01168	0.969
39DAP/27DAP	1.19289	0.337
41DAP/39DAP	1.09537	0.827
42DAP/41DAP	1.12237	0.425
43DAP/42DAP	0.95588	0.558
47DAP/43DAP	1.06099	0.699
52DAP/47DAP	0.95534	0.839
57DAP/52DAP	1.17817	0.346
57DAP/7DAP	1.39185	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11009	0.435
17DAP/reference	1.09145	0.092
27DAP/reference	1.06294	0.453
39DAP/reference	1.49481	0.005
41DAP/reference	1.46538	0.011
42DAP/reference	1.17446	0.021
43DAP/reference	1.66575	0.006
47DAP/reference	1.77193	0.019
52DAP/reference	1.86227	0.008
57DAP/reference	2.42305	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89124	0.306
17DAP/reference	0.83844	0.086
27DAP/reference	0.84401	0.064
39DAP/reference	0.97723	0.404
41DAP/reference	1.16844	0.043
42DAP/reference	1.02222	0.879
43DAP/reference	0.94949	0.438
47DAP/reference	1.17903	0.019
52DAP/reference	0.75286	0.005
57DAP/reference	0.85379	0.144

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19195	0.18
17DAP/reference	0.85421	0.205
27DAP/reference	0.87944	0.052
39DAP/reference	1.14895	0.064
41DAP/reference	0.99002	0.682
42DAP/reference	1.22957	0.029
43DAP/reference	1.21293	0.077
47DAP/reference	1.00706	0.731
52DAP/reference	1.53985	0.042
57DAP/reference	1.18111	0.2

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96891	1
26DAP/20DAP	1.55824	0.147
34DAP/26DAP	1.00373	1
51DAP/34DAP	1.47193	0.041
52DAP/51DAP	0.74598	0.151
53DAP/52DAP	N/A	N/A
55DAP/53DAP	0.72614	0.016
57DAP/55DAP	1.20089	0.764
62DAP/57DAP	0.84889	0.466
68DAP/62DAP	1.35058	0.214
68DAP/14DAP	2.49338	0.019

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.8309	0.068

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.78916	0.241
Mature Green Tomato/Ripe Tomato	1.74351	0.577
Immature Eggplant/Mature Eggplant	1.42468	0.05
Ripe Pepper/Ripe Tomato	1.35535	0.258
Mature Eggplant/Ripe Tomato	0.66585	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.89659	0.736
1-1-2/M82	1.25052	1
12-2/M82	1.04434	1
12-4/M82	1.18125	1
1-3/M82	1.52052
2-1-1/M82	1.03494	1
2-1/M82	1.03668	1
2-6/M82	1.11336	0.695
3-2/M82	0.96518	0.752
4-1-1/M82	0.8334	1
4-1/M82	1.84011
4-3-2/M82	1.12115	1
4-3/M82	0.9719	1
5-3/M82	0.9915	1
6-2/M82	0.80822	0.497
6-3/M82	1.09553	1
7-1/M82	0.95194	0.803
7-2/M82	1.09173	0.324
9-3-2/M82	1.30842	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.12709	0.365
IL2-6/WTpooled	1.01204	0.584
IL7-5/WTpooled	1.05623	0.722
IL7-3/WTpooled	1.08113	1
IL12-4/WTpooled	1.03633	0.737
IL1-4/WTpooled	1.01344	1
WT/WTpooled	1.02623	0.855

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	0.90672	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.14892	0.724
DC3000/delta hrp 6h	1.02721	1
DC3000/delta hrp 12h	1.0332	1
DC3000/delta hrp 24h	0.79163	0.087

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.13615	0.121
DC3000 delta B/DC3000 delta AB	1.25827	0.122

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.18017	1
Exp 36h	0.95124	0.879
Exp 60h	0.94289	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9383
Var 0h	0.92291	0.933
Var 12h I row2-row1	1.01858	1
Var 12h NI row2-row1	1.04015	1
Var 36h I row2-row1	1.15557	0.368
Var 36h NI row2-row1	1.0571	1
Var 60h I row2-row1	0.82403	0.582
Var 60h NI row2-row1	0.9636	0.932
Time course 0hI-0hNI	0.94325	0.582
Time course 12hI-12hNI	0.95154	0.501
Time course 36hI-36hNI	0.97495	0.533
Time course 60hI-60hNI	1.14961	0.096

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)	1.02594	0.798
transgenic ySAMdc/azygous control (breaker)	0.95971	1
transgenic ySAMdc/azygous control (red)	0.90467	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.17784	0.261

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.97897	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.11262	0.096
Manapal/WT (break)	1.22225	0.13
Manapal/WT (red)	0.8712	0.229