Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.9.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92463	0.586
27DAP/17DAP	1.29125	0.845
39DAP/27DAP	1.0012	0.682
41DAP/39DAP	1.29984	0.293
42DAP/41DAP	1.06043	0.971
43DAP/42DAP	1.47298	0.756
47DAP/43DAP	1.00674	0.859
52DAP/47DAP	1.11561	0.869
57DAP/52DAP	1.11001	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98868	0.661
17DAP/reference	1.0814	0.172
27DAP/reference	0.9759	0.581
39DAP/reference	1.1838	0.083
41DAP/reference	1.15799	0.054
42DAP/reference	0.96597	0.242
43DAP/reference	0.99666	0.882
47DAP/reference	0.96364	0.345
52DAP/reference	0.86266	0.091
57DAP/reference	0.81147	0.031

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15499	0.797
27DAP/17DAP	1.2044	0.383
39DAP/27DAP	1.05386	0.654
41DAP/39DAP	1.28288	0.705
42DAP/41DAP	1.06298	1
43DAP/42DAP	1.06489	0.585
47DAP/43DAP	1.10211	0.822
52DAP/47DAP	1.08937	0.826
57DAP/52DAP	0.94563	0.632
57DAP/7DAP	1.21752	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.73898	0.066
17DAP/reference	0.81462	0.024
27DAP/reference	0.89291	0.045
39DAP/reference	0.76166	0.013
41DAP/reference	0.73031	0.02
42DAP/reference	0.61693	0.01
43DAP/reference	0.75665	0.037
47DAP/reference	0.79325	0.04
52DAP/reference	0.72569	0.017
57DAP/reference	0.71086	0.032

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09343	0.3
17DAP/reference	1.11379	0.216
27DAP/reference	0.87322	0.134
39DAP/reference	1.04811	1
41DAP/reference	0.79213	0.011
42DAP/reference	0.78641	0.025
43DAP/reference	1.20869	0.054
47DAP/reference	0.93545	0.188
52DAP/reference	1.06286	0.498
57DAP/reference	1.2527	0.043

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80877	0.039
17DAP/reference	0.96082	0.488
27DAP/reference	0.95045	0.376
39DAP/reference	0.91184	0.083
41DAP/reference	0.89089	0.167
42DAP/reference	0.89624	0.287
43DAP/reference	0.8452	0.12
47DAP/reference	0.94473	0.371
52DAP/reference	1.16336	0.79
57DAP/reference	0.60737	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93261	0.733
26DAP/20DAP	0.86491	1
34DAP/26DAP	1.29172	1
51DAP/34DAP	1.21689	0.909
52DAP/51DAP	0.92393	1
53DAP/52DAP	1.49174	0.089
55DAP/53DAP	0.96348	0.784
57DAP/55DAP	0.93541	0.731
62DAP/57DAP	1.16233	0.833
68DAP/62DAP	1.07121	0.939
68DAP/14DAP	0.93682	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.74249	0.059

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.40726	0.102
Mature Green Tomato/Ripe Tomato	0.37409	0.026
Immature Eggplant/Mature Eggplant	1.50224	0.054
Ripe Pepper/Ripe Tomato	2.49093	1
Mature Eggplant/Ripe Tomato	4.53081	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00302	1
1-1-2/M82	0.93853	0.958
12-2/M82	0.95881	0.955
12-4/M82	1.0385	1
1-3/M82	0.95183	0.378
2-1-1/M82	1.00739	1
2-1/M82	1.32817	1
2-6/M82	0.90022	1
3-2/M82	0.91557	1
4-1-1/M82	1.00431	1
4-1/M82	0.87637
4-3-2/M82	1.17856
4-3/M82	1.00766	1
5-3/M82	0.98835	1
6-2/M82	1.07194	1
6-3/M82	1.02203	1
7-1/M82	0.90687	0.476
7-2/M82	0.86737	0.578
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.92311	0.247
IL2-6/WTpooled	0.9385	0.473
IL7-5/WTpooled	0.99294	1
IL7-3/WTpooled	0.94202	0.418
IL12-4/WTpooled	1.08218	0.695
IL1-4/WTpooled	0.96918	0.834
WT/WTpooled	1.00503	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	1.31921	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95461	1
DC3000/delta hrp 6h	0.85738	0.95
DC3000/delta hrp 12h	1.10075	1
DC3000/delta hrp 24h	0.98755	0.978

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.99178	0.046
DC3000 delta B/DC3000 delta AB	3.01864	0.086

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97633	1
Exp 36h	2.27239	0.489
Exp 60h	1.86435	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.28366	1
Var 0h	1.23359	0.98
Var 12h I row2-row1	1.24163	0.211
Var 12h NI row2-row1	1.30825	1
Var 36h I row2-row1	0.98899	1
Var 36h NI row2-row1	1.05378	1
Var 60h I row2-row1	0.71736	0.287
Var 60h NI row2-row1	0.9393	0.756
Time course 0hI-0hNI	1.13021	0.451
Time course 12hI-12hNI	1.39647	0.022
Time course 36hI-36hNI	2.23713	0.005
Time course 60hI-60hNI	11.5865	0.008

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)	0.94956	0.428
transgenic ySAMdc/azygous control (breaker)	1.10297	1
transgenic ySAMdc/azygous control (red)	1.23188	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98862	0.22

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.85262	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.8356	1
Manapal/WT (break)	0.92344	1
Manapal/WT (red)	1.06008	1