Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.4.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.33002	0.315
27DAP/17DAP	0.89004	0.749
39DAP/27DAP	1.16895	0.677
41DAP/39DAP	0.59569	0.045
42DAP/41DAP	0.96897	1
43DAP/42DAP	1.2191	0.671
47DAP/43DAP	1.12351	0.68
52DAP/47DAP	0.61453	0.137
57DAP/52DAP	0.90768	0.845

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09204	0.662
17DAP/reference	1.00276	0.904
27DAP/reference	1.1583	0.394
39DAP/reference	1.19381	0.111
41DAP/reference	1.00852	1
42DAP/reference	1.11909	0.021
43DAP/reference	1.44221	0.008
47DAP/reference	1.43657	0.001
52DAP/reference	1.07783	0.8
57DAP/reference	1.28641	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.79899	0.036
27DAP/17DAP	0.76791	0.121
39DAP/27DAP	0.77091	0.031
41DAP/39DAP	1.1274	0.853
42DAP/41DAP	0.99351	0.872
43DAP/42DAP	0.92494	0.269
47DAP/43DAP	0.84244	0.031
52DAP/47DAP	1.11772	0.573
57DAP/52DAP	0.76632	0.099
57DAP/7DAP	0.67478	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.4588	0.037
17DAP/reference	1.2837	0.016
27DAP/reference	0.91811	0.125
39DAP/reference	1.97931	0.006
41DAP/reference	1.23409	0.02
42DAP/reference	1.33295	0.016
43DAP/reference	1.53656	0.007
47DAP/reference	1.81291	0.017
52DAP/reference	1.8155	0.007
57DAP/reference	2.14451	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77069	0.119
17DAP/reference	0.98936	0.693
27DAP/reference	0.93964	0.423
39DAP/reference	1.65965	0.377
41DAP/reference	1.28336	0.076
42DAP/reference	0.9948	0.655
43DAP/reference	0.89848	0.229
47DAP/reference	1.17879	0.182
52DAP/reference	0.91993	0.04
57DAP/reference	0.65891	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.77366	0.035
17DAP/reference	1.30822	0.371
27DAP/reference	1.40095	0.019
39DAP/reference	1.9116	0.005
41DAP/reference	1.67178	0.007
42DAP/reference	2.43415	0.008
43DAP/reference	3.41088	0.006
47DAP/reference	2.37631	0.005
52DAP/reference	2.10569	0.03
57DAP/reference	2.31762	0.009

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.89982	1
26DAP/20DAP	0.7833	0.512
34DAP/26DAP	1.21735	0.819
51DAP/34DAP	0.9258	0.618
52DAP/51DAP	0.98051	1
53DAP/52DAP	0.85193	0.297
55DAP/53DAP	1.09475	0.671
57DAP/55DAP	1.14472	0.969
62DAP/57DAP	0.89678	0.871
68DAP/62DAP	1.15001	0.747
68DAP/14DAP	1.3188	0.189

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.7913	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.83402	0.29
Mature Green Tomato/Ripe Tomato	1.93099	0.016
Immature Eggplant/Mature Eggplant	0.38579	0.057
Ripe Pepper/Ripe Tomato	1.11773	1
Mature Eggplant/Ripe Tomato	0.80184	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.31504	0.742
1-1-2/M82	1.41246	1
12-2/M82	0.79588	0.862
12-4/M82	1.68397	1
1-3/M82	1.7158	0.479
2-1-1/M82	1.21474	0.689
2-1/M82	0.5571	0.519
2-6/M82	1.84245	0.329
3-2/M82	1.21789	0.967
4-1-1/M82	1.23294	1
4-1/M82	0.84667	1
4-3-2/M82	1.82106
4-3/M82	1.45724	1
5-3/M82	1.04032	1
6-2/M82	N/A	N/A
6-3/M82	0.52373	0.232
7-1/M82	0.80821	0.803
7-2/M82	1.21502	1
9-3-2/M82	1.7436

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.99218	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.05115	1
IL7-3/WTpooled	0.88632	1
IL12-4/WTpooled	1.17895	0.531
IL1-4/WTpooled	0.84419	0.834
WT/WTpooled	1.09363	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	1.08861	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08087	0.921
DC3000/delta hrp 6h	1.09348	1
DC3000/delta hrp 12h	1.07181	1
DC3000/delta hrp 24h	0.87443	0.264

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.98601	1
DC3000 delta B/DC3000 delta AB	0.93204	0.178

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.47976	1
Exp 36h	1.28167	0.943
Exp 60h	0.87596	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.84963	0.309
transgenic ySAMdc/azygous control (breaker)	1.72777	0.248
transgenic ySAMdc/azygous control (red)	1.24381	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03885	0.334

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.75971	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.48835	0.14
Manapal/WT (break)	1.60771	0.381
Manapal/WT (red)	2.46076	0.134