Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.2.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93878	0.652
27DAP/17DAP	0.85679	0.626
39DAP/27DAP	0.88441	0.564
41DAP/39DAP	1.52518	0.166
42DAP/41DAP	0.89705	1
43DAP/42DAP	1.0788	1
47DAP/43DAP	0.87648	0.634
52DAP/47DAP	0.84608	0.595
57DAP/52DAP	1.19961	0.944

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.598	0.033
17DAP/reference	0.44189	0.011
27DAP/reference	0.91544	0.428
39DAP/reference	0.62813	0.027
41DAP/reference	0.33473	0.01
42DAP/reference	1.03798	0.326
43DAP/reference	0.97856	0.708
47DAP/reference	1.18096	0.674
52DAP/reference	2.06894	0.053
57DAP/reference	2.06097	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18664	0.812
27DAP/17DAP	1.03092	0.928
39DAP/27DAP	0.91344	0.247
41DAP/39DAP	0.91501	0.764
42DAP/41DAP	1.24309	0.149
43DAP/42DAP	0.86764	0.336
47DAP/43DAP	0.8524	0.31
52DAP/47DAP	2.67499	0.048
57DAP/52DAP	2.82949	0.048
57DAP/7DAP	2.33973	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.39401	0.026
17DAP/reference	5.47542	0.006
27DAP/reference	4.5525	0.006
39DAP/reference	5.15079	0.005
41DAP/reference	5.40124	0.01
42DAP/reference	6.79079	0.006
43DAP/reference	8.11237	0.006
47DAP/reference	4.37813	0.102
52DAP/reference	5.35859	0.007
57DAP/reference	5.06141	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.53941	0.017
17DAP/reference	0.44368	0.004
27DAP/reference	0.90533	0.327
39DAP/reference	0.90479	0.306
41DAP/reference	1.10937	0.587
42DAP/reference	0.96048	0.392
43DAP/reference	0.36782	0.008
47DAP/reference	0.62559	0.019
52DAP/reference	0.71272	0.007
57DAP/reference	0.30863	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.88071	0.058
17DAP/reference	2.16668	0.956
27DAP/reference	7.2469	0.02
39DAP/reference	6.32337	0.017
41DAP/reference	4.55436	0.008
42DAP/reference	5.05409	0.007
43DAP/reference	6.66702	0.008
47DAP/reference	0.8947	0.269
52DAP/reference	5.0576	0.241
57DAP/reference	4.59202	0.085

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07352	0.966
26DAP/20DAP	1.22671	0.471
34DAP/26DAP	2.62022	0.542
51DAP/34DAP	1.27928	0.746
52DAP/51DAP	2.1298	0.089
53DAP/52DAP	0.73387	0.138
55DAP/53DAP	0.94081	0.675
57DAP/55DAP	0.36785	0.011
62DAP/57DAP	1.64417	0.034
68DAP/62DAP	15.1161	0.021
68DAP/14DAP	16.4889	0.017

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.20127	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	4.00056	0.015
Immature Eggplant/Mature Eggplant	2.40386	0.05
Ripe Pepper/Ripe Tomato	1.27286	1
Mature Eggplant/Ripe Tomato	1.30191	1

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	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	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	1.02468	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.90222	0.418
IL12-4/WTpooled	1.13364	0.785
IL1-4/WTpooled	0.91835
WT/WTpooled	1.01273	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	1.10605	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.13237	0.846
DC3000/delta hrp 6h	1.02217	1
DC3000/delta hrp 12h	1.16104	1
DC3000/delta hrp 24h	0.43433	0.034

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	1.84688	0.079

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89252	1
Exp 36h	0.86125	0.623
Exp 60h	0.74397	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98311	1
Var 0h	0.99827	1
Var 12h I row2-row1	0.81935	0.627
Var 12h NI row2-row1	1.12058	1
Var 36h I row2-row1	1.18229	1
Var 36h NI row2-row1	2.21476	0.482
Var 60h I row2-row1	1.08364	1
Var 60h NI row2-row1	1.12984	1
Time course 0hI-0hNI	0.8855	0.415
Time course 12hI-12hNI	0.93756	0.705
Time course 36hI-36hNI	0.81687	0.153
Time course 60hI-60hNI	0.60382	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)	1.03727	0.511
transgenic ySAMdc/azygous control (breaker)	1.62885	0.248
transgenic ySAMdc/azygous control (red)	1.25429	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0208	0.495

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.05786	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.1371	1
Manapal/WT (break)	0.93306	0.299
Manapal/WT (red)	1.23573	0.413