Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.13.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18857	0.394
27DAP/17DAP	1.35612	0.73
39DAP/27DAP	0.90873	0.652
41DAP/39DAP	1.02216	0.978
42DAP/41DAP	0.95265	1
43DAP/42DAP	1.22246	0.918
47DAP/43DAP	1.23282	0.502
52DAP/47DAP	1.06778	0.96
57DAP/52DAP	0.8754	0.919

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90971	0.3
17DAP/reference	1.13392	0.026
27DAP/reference	0.98075	0.683
39DAP/reference	1.07428	0.218
41DAP/reference	1.14705	0.171
42DAP/reference	0.928	0.075
43DAP/reference	1.10254	0.044
47DAP/reference	1.17301	0.119
52DAP/reference	1.13948	0.498
57DAP/reference	0.88176	0.068

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.76679	0.323
27DAP/17DAP	0.99002	0.943
39DAP/27DAP	1.14789	0.636
41DAP/39DAP	0.96233	0.968
42DAP/41DAP	1.03811	0.865
43DAP/42DAP	1.16482	0.446
47DAP/43DAP	1.11115	0.749
52DAP/47DAP	2.71782	0.044
57DAP/52DAP	5.14769	0.033
57DAP/7DAP	1.99928	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10196	0.461
17DAP/reference	1.39653	0.006
27DAP/reference	1.53835	0.01
39DAP/reference	1.35852	0.006
41DAP/reference	1.57755	0.012
42DAP/reference	1.40501	0.037
43DAP/reference	1.72611	0.008
47DAP/reference	1.10769	0.98
52DAP/reference	1.5864	0.011
57DAP/reference	1.37683	0.094

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99998	0.811
17DAP/reference	0.87114	0.026
27DAP/reference	0.91681	0.304
39DAP/reference	0.87998	0.195
41DAP/reference	0.84009	0.231
42DAP/reference	0.93185	0.261
43DAP/reference	0.92177	0.298
47DAP/reference	1.07657	0.274
52DAP/reference	0.88972	0.086
57DAP/reference	1.17678	0.089

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12393	0.237
17DAP/reference	1.10599	0.728
27DAP/reference	1.84457	0.013
39DAP/reference	1.61309	0.021
41DAP/reference	1.27629	0.058
42DAP/reference	1.08294	0.836
43DAP/reference	0.91224	0.398
47DAP/reference	1.19457	0.12
52DAP/reference	1.54055	0.08
57DAP/reference	1.55285	0.083

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93293	1
26DAP/20DAP	0.70382	0.512
34DAP/26DAP	1.87055
51DAP/34DAP	3.93889	0.581
52DAP/51DAP	0.90542	1
53DAP/52DAP	1.61362	0.212
55DAP/53DAP	1.09298	0.562
57DAP/55DAP	0.96635	0.795
62DAP/57DAP	0.92602	0.871
68DAP/62DAP	1.04415	0.81
68DAP/14DAP	0.56928	0.056

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.52882	0.025

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.03979	0.021
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.13961	0.224
Mature Eggplant/Ripe Tomato	0.19868	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.1245	0.877
1-1-2/M82	1.00522	1
12-2/M82	1.53094
12-4/M82	N/A	N/A
1-3/M82	0.76074
2-1-1/M82	1.19928
2-1/M82	N/A	N/A
2-6/M82	1.32342
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	0.97834
4-3-2/M82	N/A	N/A
4-3/M82	1.49189
5-3/M82	0.58174	0.419
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.16862
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	1.05106	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.94848	1
IL12-4/WTpooled	0.94979	1
IL1-4/WTpooled	1.12819	1
WT/WTpooled	1.03246	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	0.8502	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.12964	0.921
DC3000/delta hrp 6h	1.59097
DC3000/delta hrp 12h	0.98854	1
DC3000/delta hrp 24h	1.30206	0.336

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.99011	1
Exp 36h	0.85338	0.749
Exp 60h	1.03018	1

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	0.97696	1
Var 12h I row2-row1	1.17008	0.216
Var 12h NI row2-row1	1.01202	1
Var 36h I row2-row1	0.99033	0.805
Var 36h NI row2-row1	1.22388	0.482
Var 60h I row2-row1	1.0804
Var 60h NI row2-row1	0.66638	1
Time course 0hI-0hNI	1.01255	0.852
Time course 12hI-12hNI	1.21352	0.281
Time course 36hI-36hNI	1.3888	0.004
Time course 60hI-60hNI	1.57247	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)	1.22049	0.325
transgenic ySAMdc/azygous control (breaker)	0.42204	0.139
transgenic ySAMdc/azygous control (red)	0.87331	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97958	0.334

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.41862	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.63619	1
Manapal/WT (break)	1.01526	1
Manapal/WT (red)	0.85791	0.503