Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.20.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05451	0.858
27DAP/17DAP	1.16744	0.845
39DAP/27DAP	0.99458	0.733
41DAP/39DAP	0.71637	0.166
42DAP/41DAP	1.05929	1
43DAP/42DAP	0.83449	0.705
47DAP/43DAP	1.29414	0.842
52DAP/47DAP	1.21855	0.804
57DAP/52DAP	0.96968	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	N/A	N/A
17DAP/reference	0.15436
27DAP/reference	1.1979
39DAP/reference	4.2876	0.679
41DAP/reference	0.53036
42DAP/reference	N/A	N/A
43DAP/reference	N/A	N/A
47DAP/reference	N/A	N/A
52DAP/reference	6.67589
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.24429	0.508
27DAP/17DAP	1.03695	0.96
39DAP/27DAP	1.17974	0.214
41DAP/39DAP	1.10668	0.861
42DAP/41DAP	1.05957	0.886
43DAP/42DAP	0.93562	0.538
47DAP/43DAP	1.10329	0.772
52DAP/47DAP	0.97324	0.902
57DAP/52DAP	1.06866	0.714
57DAP/7DAP	1.39883	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89912	0.168
17DAP/reference	0.77634	0.014
27DAP/reference	1.01319	0.974
39DAP/reference	0.832	0.025
41DAP/reference	0.90441	0.146
42DAP/reference	0.84755	0.034
43DAP/reference	0.93761	0.183
47DAP/reference	1.11485	0.504
52DAP/reference	0.94168	0.254
57DAP/reference	1.00437	0.804

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79618	0.093
17DAP/reference	0.93307	0.214
27DAP/reference	1.19274	0.404
39DAP/reference	0.90346	0.322
41DAP/reference	0.79046	0.052
42DAP/reference	1.1456
43DAP/reference	1.22791	0.605
47DAP/reference	N/A	N/A
52DAP/reference	0.79373	0.02
57DAP/reference	1.05258	0.593

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91396	0.268
17DAP/reference	0.95423	0.537
27DAP/reference	0.8971	0.078
39DAP/reference	0.9351	0.133
41DAP/reference	0.92771	0.331
42DAP/reference	0.89936	0.172
43DAP/reference	0.89755	0.158
47DAP/reference	1.01054	0.731
52DAP/reference	1.05476	0.89
57DAP/reference	1.75988	0.032

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98377	1
26DAP/20DAP	0.94284	1
34DAP/26DAP	1.48842	0.819
51DAP/34DAP	0.8715	0.667
52DAP/51DAP	1.33607	0.836
53DAP/52DAP	1.12316	0.797
55DAP/53DAP	1.40757	0.689
57DAP/55DAP	0.93653	0.736
62DAP/57DAP	1.34517	0.303
68DAP/62DAP	1.10432	0.939
68DAP/14DAP	2.26519	0.236

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.23474	0.627

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.63115
Mature Green Tomato/Ripe Tomato	1.21535	0.523
Immature Eggplant/Mature Eggplant	1.16362
Ripe Pepper/Ripe Tomato	0.86891	1
Mature Eggplant/Ripe Tomato	0.79858	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01185	1
1-1-2/M82	1.00028	1
12-2/M82	1.42156
12-4/M82	1.03616	1
1-3/M82	0.95191	1
2-1-1/M82	1.07451	1
2-1/M82	1.18214	1
2-6/M82	1.02954	1
3-2/M82	0.76474
4-1-1/M82	1.25747	0.968
4-1/M82	1.09655	1
4-3-2/M82	1.06554	1
4-3/M82	0.96579	1
5-3/M82	0.91521	1
6-2/M82	0.71271	0.497
6-3/M82	0.97353	1
7-1/M82	0.64416
7-2/M82	0.90044	0.881
9-3-2/M82	1.13382	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.51098	0.277
IL2-6/WTpooled	0.99269	1
IL7-5/WTpooled	0.55621
IL7-3/WTpooled	1.41601	1
IL12-4/WTpooled	1.32802	0.516
IL1-4/WTpooled	1.03185	1
WT/WTpooled	0.8694	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	0.86829

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02601	0.921
DC3000/delta hrp 6h	0.81622	0.95
DC3000/delta hrp 12h	1.07005	1
DC3000/delta hrp 24h	1.05032	0.453

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.20796
DC3000 delta B/DC3000 delta AB	0.8364	0.605

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.24438	1
Exp 36h	1.31742	0.693
Exp 60h	1.44366	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05401	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.11726	0.215
Var 12h NI row2-row1	0.95193	0.906
Var 36h I row2-row1	1.01222	1
Var 36h NI row2-row1	1.01683	0.852
Var 60h I row2-row1	0.99765	1
Var 60h NI row2-row1	0.98384	1
Time course 0hI-0hNI	1.07871	0.719
Time course 12hI-12hNI	1.38921	0.1
Time course 36hI-36hNI	2.27053	0.005
Time course 60hI-60hNI	2.9117	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)	1.15647	0.571
transgenic ySAMdc/azygous control (breaker)	0.45082	0.131
transgenic ySAMdc/azygous control (red)	0.80878	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.2624	0.105
Manapal/WT (break)	1.47914	1
Manapal/WT (red)	1.21395	0.413