Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.17.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.21435	0.498
27DAP/17DAP	0.87925	0.713
39DAP/27DAP	1.45464	0.287
41DAP/39DAP	0.92771	0.724
42DAP/41DAP	1.20027	1
43DAP/42DAP	1.17052	0.873
47DAP/43DAP	0.61143	0.097
52DAP/47DAP	1.11775	0.869
57DAP/52DAP	1.10981	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17355	0.366
17DAP/reference	1.40149	0.127
27DAP/reference	1.15255	0.847
39DAP/reference	1.12713	0.377
41DAP/reference	1.20397	0.024
42DAP/reference	1.4331	0.003
43DAP/reference	1.02159	0.838
47DAP/reference	1.37153	0.009
52DAP/reference	1.29416	0.205
57DAP/reference	1.3236	0.063

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.38921	0.422
27DAP/17DAP	1.19185	0.604
39DAP/27DAP	1.05293	0.811
41DAP/39DAP	1.17894	0.801
42DAP/41DAP	0.95086	0.69
43DAP/42DAP	0.83953	0.197
47DAP/43DAP	2.3944	0.812
52DAP/47DAP	1.67568	0.19
57DAP/52DAP	1.57955	0.103
57DAP/7DAP	1.04006	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.44177	0.056
17DAP/reference	1.1564	0.574
27DAP/reference	1.02078	1
39DAP/reference	1.51481	0.032
41DAP/reference	0.98338	0.565
42DAP/reference	0.90269	0.338
43DAP/reference	0.88999	0.139
47DAP/reference	1.06995	0.915
52DAP/reference	0.97388	0.477
57DAP/reference	1.13522	0.094

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99307	0.58
17DAP/reference	1.19171	0.216
27DAP/reference	1.36889	0.195
39DAP/reference	1.07862	0.912
41DAP/reference	1.20273	0.157
42DAP/reference	1.29873	0.39
43DAP/reference	1.37912	0.192
47DAP/reference	1.35449	0.015
52DAP/reference	1.06381	0.702
57DAP/reference	0.96352	0.549

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10008	0.602
17DAP/reference	1.07988	0.685
27DAP/reference	1.05869	0.749
39DAP/reference	1.04511	0.483
41DAP/reference	0.8787	0.096
42DAP/reference	1.17353	0.45
43DAP/reference	1.16735	0.186
47DAP/reference	1.29722	0.228
52DAP/reference	1.02288	0.904
57DAP/reference	1.3181	0.141

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.13052	1
26DAP/20DAP	1.49735	0.308
34DAP/26DAP	1.07472	0.819
51DAP/34DAP	1.96385	0.038
52DAP/51DAP	0.85405	1
53DAP/52DAP	2.13484	0.021
55DAP/53DAP	0.81788	0.125
57DAP/55DAP	1.12434	0.969
62DAP/57DAP	0.51931	0.005
68DAP/62DAP	0.91896	0.722
68DAP/14DAP	0.83766	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.41675	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.69654	0.187
Mature Green Tomato/Ripe Tomato	2.02704	0.017
Immature Eggplant/Mature Eggplant	0.70369	0.067
Ripe Pepper/Ripe Tomato	3.21796	0.258
Mature Eggplant/Ripe Tomato	3.18455	0.26

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	0.89002	1
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	N/A	N/A
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	1.10056	1
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	1.00384	1
IL2-6/WTpooled	0.87396	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.27248	1
IL12-4/WTpooled	0.86436	1
IL1-4/WTpooled	0.84475	0.834
WT/WTpooled	1.10185	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	0.89455	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97817	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.30493	1
DC3000/delta hrp 24h	1.17945	0.088

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.98481	1
DC3000 delta B/DC3000 delta AB	1.12507	0.335

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.90567	1
Exp 36h	1.1248	1
Exp 60h	1.16572	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0339	1
Var 0h	1.0674	1
Var 12h I row2-row1	1.06901	0.544
Var 12h NI row2-row1	1.13846	0.34
Var 36h I row2-row1	0.91958	1
Var 36h NI row2-row1	1.14255	1
Var 60h I row2-row1	0.70787	0.293
Var 60h NI row2-row1	1.03593	1
Time course 0hI-0hNI	1.02549	1
Time course 12hI-12hNI	0.98913	0.956
Time course 36hI-36hNI	1.01287	0.841
Time course 60hI-60hNI	1.22541	0.115

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)	0.99525	0.931
transgenic ySAMdc/azygous control (breaker)	0.87156	0.251
transgenic ySAMdc/azygous control (red)	0.80984	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	0.65695	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.70343	0.172
Manapal/WT (break)	0.93465	1
Manapal/WT (red)	0.97919	0.863