Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.4.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88952	0.211
27DAP/17DAP	1.01169	0.926
39DAP/27DAP	0.90485	0.462
41DAP/39DAP	1.00401	0.96
42DAP/41DAP	0.95474	1
43DAP/42DAP	0.94122	0.801
47DAP/43DAP	0.95994	0.847
52DAP/47DAP	1.01047	0.984
57DAP/52DAP	1.04551	0.904

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17209	0.052
17DAP/reference	0.97671	0.664
27DAP/reference	1.03487	0.672
39DAP/reference	0.95514	0.779
41DAP/reference	0.91814	0.542
42DAP/reference	1.05801	0.299
43DAP/reference	0.92754	0.691
47DAP/reference	1.0619	0.04
52DAP/reference	0.85591	0.075
57DAP/reference	1.77438

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88244	0.148
27DAP/17DAP	1.05349	0.74
39DAP/27DAP	0.95883	0.507
41DAP/39DAP	0.92223	0.193
42DAP/41DAP	0.98113	0.774
43DAP/42DAP	1.02993	0.351
47DAP/43DAP	0.98441	0.87
52DAP/47DAP	1.00178	1
57DAP/52DAP	0.93716	0.546
57DAP/7DAP	0.97926	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31648	0.049
17DAP/reference	1.03158	0.688
27DAP/reference	0.89408	0.045
39DAP/reference	1.00498	1
41DAP/reference	1.02353	0.577
42DAP/reference	1.01717	0.405
43DAP/reference	1.01984	0.873
47DAP/reference	0.94224	0.293
52DAP/reference	0.99182	0.621
57DAP/reference	1.02167	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06668	0.093
17DAP/reference	1.02518	0.543
27DAP/reference	1.04259	1
39DAP/reference	0.97383	0.485
41DAP/reference	1.01008	1
42DAP/reference	0.89409	0.012
43DAP/reference	1.04187	0.751
47DAP/reference	0.92838	0.102
52DAP/reference	0.94323	0.055
57DAP/reference	0.95654	0.408

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32446	0.021
17DAP/reference	1.08894	0.215
27DAP/reference	1.04421	0.325
39DAP/reference	0.93148	0.046
41DAP/reference	0.99961	1
42DAP/reference	0.82905	0.025
43DAP/reference	0.90573	0.019
47DAP/reference	0.94983	0.286
52DAP/reference	0.91135	0.242
57DAP/reference	0.89482	0.036

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01878	0.966
26DAP/20DAP	0.97638	1
34DAP/26DAP	0.95649	0.702
51DAP/34DAP	0.88697	0.161
52DAP/51DAP	1.03406	0.662
53DAP/52DAP	1.0009	0.97
55DAP/53DAP	0.89522	0.293
57DAP/55DAP	1.15395	0.826
62DAP/57DAP	0.80019	0.002
68DAP/62DAP	1.14039	0.827
68DAP/14DAP	0.95477	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.85286	0.092

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.61233	0.058
Mature Green Tomato/Ripe Tomato	1.06018	0.948
Immature Eggplant/Mature Eggplant	0.39957	0.062
Ripe Pepper/Ripe Tomato	3.74573	1
Mature Eggplant/Ripe Tomato	11.4991	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98637	0.961
1-1-2/M82	0.99888	1
12-2/M82	0.95097	0.955
12-4/M82	1.05556	1
1-3/M82	1.00367	1
2-1-1/M82	0.92263	0.683
2-1/M82	0.93096	1
2-6/M82	0.97202	1
3-2/M82	1.01066	0.967
4-1-1/M82	0.96561	1
4-1/M82	1.09303	1
4-3-2/M82	0.90373	1
4-3/M82	0.96549	0.72
5-3/M82	1.02946	1
6-2/M82	1.07381	1
6-3/M82	1.01397	1
7-1/M82	1.03005	1
7-2/M82	1.00857	1
9-3-2/M82	0.91042	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	0.85862	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93892	0.868
DC3000/delta hrp 6h	0.81375
DC3000/delta hrp 12h	0.92062	1
DC3000/delta hrp 24h	0.77554	0.131

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.57381	0.03
DC3000 delta B/DC3000 delta AB	0.66189	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07655	1
Exp 36h	0.86033	0.623
Exp 60h	0.84827	0.29

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95517	1
Var 0h	0.97029	1
Var 12h I row2-row1	0.89166	0.467
Var 12h NI row2-row1	1.0228	1
Var 36h I row2-row1	0.87273	0.805
Var 36h NI row2-row1	0.97212	0.743
Var 60h I row2-row1	1.53952	0.562
Var 60h NI row2-row1	1.03103	0.904
Time course 0hI-0hNI	0.98319	0.94
Time course 12hI-12hNI	1.02177	0.818
Time course 36hI-36hNI	1.13832	0.063
Time course 60hI-60hNI	0.36003	0.015

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)	0.81178	0.324
transgenic ySAMdc/azygous control (breaker)	1.10215	1
transgenic ySAMdc/azygous control (red)	1.05189	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.87364	0.063

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.90533	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.15393	1
Manapal/WT (break)	1.20585	1
Manapal/WT (red)	1.09524	1