Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.3.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.07397	0.053
27DAP/17DAP	1.3318	0.688
39DAP/27DAP	1.33379	0.318
41DAP/39DAP	0.65168	0.073
42DAP/41DAP	1.07034	1
43DAP/42DAP	1.12035	0.976
47DAP/43DAP	1.1577	0.595
52DAP/47DAP	0.89543	0.72
57DAP/52DAP	1.2722	0.731

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26818	0.03
17DAP/reference	0.8225	0.224
27DAP/reference	0.74883	0.048
39DAP/reference	0.64776	0.004
41DAP/reference	0.67931	0.018
42DAP/reference	0.98992	0.517
43DAP/reference	0.76643	0.015
47DAP/reference	1.68152	0.003
52DAP/reference	2.40918	0.007
57DAP/reference	0.60261

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.11924	0.036
27DAP/17DAP	1.10229	0.506
39DAP/27DAP	0.91881	0.477
41DAP/39DAP	1.21549	0.883
42DAP/41DAP	1.0674	0.783
43DAP/42DAP	0.87758	0.038
47DAP/43DAP	0.99404	0.977
52DAP/47DAP	1.17946	0.489
57DAP/52DAP	1.00704	0.881
57DAP/7DAP	1.15744	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.33283	0.031
17DAP/reference	1.29995	0.049
27DAP/reference	1.03716	1
39DAP/reference	1.19176	0.511
41DAP/reference	1.12989	0.767
42DAP/reference	1.3963	0.018
43DAP/reference	1.18206	0.212
47DAP/reference	1.2655	0.021
52DAP/reference	1.17579	0.212
57DAP/reference	0.94626	0.232

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12146	0.507
17DAP/reference	1.19674	0.156
27DAP/reference	1.10875	0.888
39DAP/reference	1.02166	0.722
41DAP/reference	1.10289	0.629
42DAP/reference	1.22467	0.144
43DAP/reference	0.83044	0.166
47DAP/reference	1.04383	0.603
52DAP/reference	0.96404	0.469
57DAP/reference	0.85506	0.107

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20604	0.207
17DAP/reference	0.9927	0.778
27DAP/reference	1.16538	0.298
39DAP/reference	1.05898	0.318
41DAP/reference	1.00711	0.826
42DAP/reference	1.11692	0.566
43DAP/reference	1.06923	0.565
47DAP/reference	1.03597	1
52DAP/reference	2.586	0.161
57DAP/reference	1.89856	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08905	0.966
26DAP/20DAP	1.23198	0.477
34DAP/26DAP	1.06344	1
51DAP/34DAP	1.54215	0.032
52DAP/51DAP	0.64593	0.151
53DAP/52DAP	1.30362	0.138
55DAP/53DAP	0.81946	0.263
57DAP/55DAP	1.26142	0.694
62DAP/57DAP	0.8372	0.466
68DAP/62DAP	1.26356	0.481
68DAP/14DAP	1.53136	0.103

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.51632	0.024

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.82261	0.276
Mature Green Tomato/Ripe Tomato	1.15122	0.69
Immature Eggplant/Mature Eggplant	0.69454	0.064
Ripe Pepper/Ripe Tomato	0.32297	0.293
Mature Eggplant/Ripe Tomato	0.30138	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.40101
12-2/M82	N/A	N/A
12-4/M82	1.19278	1
1-3/M82	N/A	N/A
2-1-1/M82	4.18208
2-1/M82	1.01755
2-6/M82	1.7992
3-2/M82	1.81292
4-1-1/M82	3.36029
4-1/M82	2.8057
4-3-2/M82	1.70798	1
4-3/M82	1.55574	1
5-3/M82	0.90961	1
6-2/M82	4.19945
6-3/M82	0.28502
7-1/M82	1.23593	1
7-2/M82	N/A	N/A
9-3-2/M82	1.08209	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.78309	0.321
IL2-6/WTpooled	1.27064	0.419
IL7-5/WTpooled	0.95107	1
IL7-3/WTpooled	0.99654	1
IL12-4/WTpooled	0.98911	1
IL1-4/WTpooled	0.97471	1
WT/WTpooled	0.96988	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	1.19017	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03984	1
DC3000/delta hrp 6h	0.94999	0.95
DC3000/delta hrp 12h	1.04259	1
DC3000/delta hrp 24h	2.34837	0.032

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.47866	0.025
DC3000 delta B/DC3000 delta AB	0.76745	0.178

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88745	1
Exp 36h	1.28427	0.693
Exp 60h	1.25632	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97609	1
Var 0h	0.93267	1
Var 12h I row2-row1	0.72883
Var 12h NI row2-row1	1.02673	1
Var 36h I row2-row1	1.13903	1
Var 36h NI row2-row1	1.03894	1
Var 60h I row2-row1	1.05124
Var 60h NI row2-row1	1.02111	1
Time course 0hI-0hNI	0.94102	0.671
Time course 12hI-12hNI	0.97176	0.827
Time course 36hI-36hNI	0.9017	0.194
Time course 60hI-60hNI	1.04489	0.673

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)	1.27196	0.256
transgenic ySAMdc/azygous control (breaker)	1.40904	0.172
transgenic ySAMdc/azygous control (red)	0.99729	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.14097	0.042

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.66385	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.93367	1
Manapal/WT (break)	0.73124	1
Manapal/WT (red)	1.13007	1