Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.17.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92767	0.551
27DAP/17DAP	0.96829	0.941
39DAP/27DAP	1.0187	0.876
41DAP/39DAP	0.91733	0.602
42DAP/41DAP	0.68069	0.397
43DAP/42DAP	1.14796	0.867
47DAP/43DAP	0.86747	0.568
52DAP/47DAP	1.22518	0.906
57DAP/52DAP	1.22515	0.859

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24107	1
17DAP/reference	1.73178	0.22
27DAP/reference	1.11457	0.239
39DAP/reference	1.10716	0.486
41DAP/reference	1.02132	0.91
42DAP/reference	1.15894	0.137
43DAP/reference	0.9396	0.519
47DAP/reference	1.13176	0.254
52DAP/reference	1.35819	0.176
57DAP/reference	1.31239	0.109

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94972	0.56
27DAP/17DAP	0.96052	0.724
39DAP/27DAP	0.88824	0.3
41DAP/39DAP	1.11346	0.861
42DAP/41DAP	0.9328	0.439
43DAP/42DAP	0.93197	0.522
47DAP/43DAP	0.9634	0.796
52DAP/47DAP	0.68902	0.105
57DAP/52DAP	1.17462	0.284
57DAP/7DAP	0.47908	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74729	0.059
17DAP/reference	0.70433	0.011
27DAP/reference	0.72659	0.01
39DAP/reference	0.7714	0.012
41DAP/reference	0.75554	0.017
42DAP/reference	0.70709	0.012
43DAP/reference	0.71634	0.015
47DAP/reference	0.96418	0.671
52DAP/reference	0.95886	0.363
57DAP/reference	0.82842	0.034

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02873	0.979
17DAP/reference	0.85842	0.106
27DAP/reference	0.99362	0.598
39DAP/reference	1.08709	1
41DAP/reference	1.23853	0.353
42DAP/reference	1.05136	0.794
43DAP/reference	0.90773	0.32
47DAP/reference	1.21451	0.426
52DAP/reference	1.11196	0.629
57DAP/reference	0.83487	0.318

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83705	0.197
17DAP/reference	0.98313	0.696
27DAP/reference	0.69194	0.021
39DAP/reference	0.83724	0.033
41DAP/reference	0.90489	0.331
42DAP/reference	1.01417	0.816
43DAP/reference	1.04018	0.827
47DAP/reference	1.10864	0.519
52DAP/reference	0.7757	0.238
57DAP/reference	1.34883	0.052

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.24669	1
26DAP/20DAP	2.66299	0.101
34DAP/26DAP	0.9683	0.954
51DAP/34DAP	0.82214	0.333
52DAP/51DAP	1.14364	0.096
53DAP/52DAP	0.98623	0.924
55DAP/53DAP	0.92551	0.663
57DAP/55DAP	0.86918	0.539
62DAP/57DAP	1.03533	1
68DAP/62DAP	3.55857	0.383
68DAP/14DAP	1.38527	0.211

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.59457	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.51484	0.149
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.95906
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

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	0.99583
IL12-4/WTpooled	1.21702	0.516
IL1-4/WTpooled	1.00561	1
WT/WTpooled	1.14628	0.999

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	1.04856	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	N/A	N/A

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.47867	0.055
DC3000 delta B/DC3000 delta AB	1.46131	0.101

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99502	1
Var 0h	1.0003	1
Var 12h I row2-row1	0.94435	0.77
Var 12h NI row2-row1	1.09284	1
Var 36h I row2-row1	1.39449	0.41
Var 36h NI row2-row1	1.00528	1
Var 60h I row2-row1	0.70899	0.439
Var 60h NI row2-row1	0.87988	0.69
Time course 0hI-0hNI	1.12197	0.764
Time course 12hI-12hNI	1.04668	0.81
Time course 36hI-36hNI	1.57023	0.009
Time course 60hI-60hNI	1.64937	0.017

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	0.93873	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.31865	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	0.73418	0.333
Manapal/WT (red)	1.08787	0.413