Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.3.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00768	0.683
27DAP/17DAP	0.93662	0.877
39DAP/27DAP	1.18514	0.691
41DAP/39DAP	0.91714	0.636
42DAP/41DAP	0.81055	0.774
43DAP/42DAP	1.109	0.906
47DAP/43DAP	0.97918	0.89
52DAP/47DAP	0.97135	0.89
57DAP/52DAP	1.20387	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19015	0.055
17DAP/reference	0.67214	0.013
27DAP/reference	0.8793	0.075
39DAP/reference	0.85388	0.031
41DAP/reference	0.66114	0.009
42DAP/reference	1.13484	0.585
43DAP/reference	0.98468
47DAP/reference	1.36917	0.01
52DAP/reference	2.13652	0.083
57DAP/reference	1.0139	0.845

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.59069	0.036
27DAP/17DAP	1.03839	0.968
39DAP/27DAP	1.0919	0.581
41DAP/39DAP	1.18588	1
42DAP/41DAP	1.05261	0.976
43DAP/42DAP	0.83948	0.224
47DAP/43DAP	1.043	0.906
52DAP/47DAP	1.08831	0.789
57DAP/52DAP	1.17363	0.374
57DAP/7DAP	1.15084	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3588	0.108
17DAP/reference	1.00593	1
27DAP/reference	1.1971	0.02
39DAP/reference	1.13061	0.009
41DAP/reference	1.04242	0.655
42DAP/reference	1.10958	0.174
43DAP/reference	1.1532	0.093
47DAP/reference	1.74592	0.014
52DAP/reference	1.22406	0.171
57DAP/reference	1.08297	0.356

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02667	1
17DAP/reference	0.89218	0.279
27DAP/reference	1.63216	0.156
39DAP/reference	1.19815	0.639
41DAP/reference	1.19276	0.035
42DAP/reference	1.39952	0.081
43DAP/reference	0.95935	0.494
47DAP/reference	1.18146	0.621
52DAP/reference	0.60213	0.003
57DAP/reference	0.67374	0.024

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17887	0.134
17DAP/reference	0.8505	0.194
27DAP/reference	0.99928	0.883
39DAP/reference	1.28338	0.008
41DAP/reference	1.05979	0.306
42DAP/reference	1.38397	0.016
43DAP/reference	1.28837	0.082
47DAP/reference	1.06689	0.966
52DAP/reference	1.31964	0.067
57DAP/reference	2.98603	0.005

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.27533	0.752
26DAP/20DAP	1.50281	0.196
34DAP/26DAP	0.96979	0.944
51DAP/34DAP	2.19099	0.032
52DAP/51DAP	0.99605	1
53DAP/52DAP	1.2604	0.212
55DAP/53DAP	0.71692	0.045
57DAP/55DAP	0.78897	0.234
62DAP/57DAP	0.60505	0.01
68DAP/62DAP	1.70432	0.027
68DAP/14DAP	2.93742	0.019

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.24159	0.264

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.87416	0.371
Mature Green Tomato/Ripe Tomato	2.38625	0.022
Immature Eggplant/Mature Eggplant	1.64036	0.05
Ripe Pepper/Ripe Tomato	1.25786	1
Mature Eggplant/Ripe Tomato	1.08515	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.68015
1-1-2/M82	N/A	N/A
12-2/M82	0.91646
12-4/M82	0.81532	0.619
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	0.73572	0.345
2-6/M82	0.72047	0.501
3-2/M82	1.70973
4-1-1/M82	0.50286
4-1/M82	N/A	N/A
4-3-2/M82	0.84724
4-3/M82	1.13476	1
5-3/M82	1.27432	0.572
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.79623
7-2/M82	N/A	N/A
9-3-2/M82	1.01529

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.87837	0.243
IL2-6/WTpooled	0.92196	1
IL7-5/WTpooled	1.2915	0.792
IL7-3/WTpooled	1.09664	1
IL12-4/WTpooled	1.02343	0.891
IL1-4/WTpooled	1.04612	1
WT/WTpooled	1.01039	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	0.81316	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01033	1
DC3000/delta hrp 6h	0.957	0.95
DC3000/delta hrp 12h	0.95599	1
DC3000/delta hrp 24h	0.63498	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.69868	0.023
DC3000 delta B/DC3000 delta AB	0.79069	0.05

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02677	1
Exp 36h	1.01868	1
Exp 60h	1.07978	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0274	1
Var 0h	0.96027	1
Var 12h I row2-row1	0.92172	0.705
Var 12h NI row2-row1	1.01968	1
Var 36h I row2-row1	1.04819	0.742
Var 36h NI row2-row1	1.40755	1
Var 60h I row2-row1	0.74547	0.374
Var 60h NI row2-row1	1.2409	0.904
Time course 0hI-0hNI	0.93398	0.555
Time course 12hI-12hNI	1.02443	0.868
Time course 36hI-36hNI	0.81619	0.052
Time course 60hI-60hNI	0.36414	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)	0.86602	0.391
transgenic ySAMdc/azygous control (breaker)	0.55674	0.15
transgenic ySAMdc/azygous control (red)	0.91472	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.25286	0.045

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.84903	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.04515	1
Manapal/WT (break)	1.55216	0.183
Manapal/WT (red)	1.12199	0.15