Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.4.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.2899	0.255
27DAP/17DAP	0.5131	0.035
39DAP/27DAP	0.56741	0.216
41DAP/39DAP	0.70666	0.127
42DAP/41DAP	0.63189	0.397
43DAP/42DAP	1.10845	1
47DAP/43DAP	0.71643	0.221
52DAP/47DAP	1.24656	0.76
57DAP/52DAP	0.96993	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74923	0.043
17DAP/reference	0.77747	0.013
27DAP/reference	0.73175	0.021
39DAP/reference	0.62091	0.047
41DAP/reference	0.62292	0.008
42DAP/reference	0.61082	0.001
43DAP/reference	0.63812	0.014
47DAP/reference	0.53545	0.001
52DAP/reference	0.46577	0.012
57DAP/reference	0.54863	0.012

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.28723
27DAP/17DAP	0.67344	0.39
39DAP/27DAP	2.88891	0.076
41DAP/39DAP	1.21081	0.799
42DAP/41DAP	1.43556	0.651
43DAP/42DAP	1.1816	1
47DAP/43DAP	N/A	N/A
52DAP/47DAP	1.09859
57DAP/52DAP	0.96174	0.813
57DAP/7DAP	0.76422

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13898	0.231
17DAP/reference	0.83608	0.025
27DAP/reference	0.53404	0.01
39DAP/reference	0.45381	0.011
41DAP/reference	0.3375	0.009
42DAP/reference	0.28493	0.01
43DAP/reference	0.30641	0.009
47DAP/reference	0.368	0.03
52DAP/reference	0.3461	0.011
57DAP/reference	0.32002	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.52756	0.006
17DAP/reference	0.46441	0.01
27DAP/reference	0.59369	0.017
39DAP/reference	0.42228	0.007
41DAP/reference	0.60253	0.028
42DAP/reference	0.61453	0.012
43DAP/reference	0.50642	0.014
47DAP/reference	0.55882	0.009
52DAP/reference	0.47031	0.004
57DAP/reference	0.3869	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.31799	0.016
17DAP/reference	1.78619	0.151
27DAP/reference	1.42422	0.057
39DAP/reference	1.15783	0.203
41DAP/reference	0.69493	0.021
42DAP/reference	0.52562	0.023
43DAP/reference	0.49828	0.016
47DAP/reference	0.50942	0.004
52DAP/reference	0.43841	0.043
57DAP/reference	0.8523	0.149

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95448	1
26DAP/20DAP	0.5214
34DAP/26DAP	0.70937
51DAP/34DAP	0.66272	0.292
52DAP/51DAP	0.93665	1
53DAP/52DAP	1.98303	0.149
55DAP/53DAP	1.55611	0.29
57DAP/55DAP	1.08169	0.97
62DAP/57DAP	1.38582	0.133
68DAP/62DAP	0.75653	0.29
68DAP/14DAP	0.58311	0.09

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	N/A	N/A

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.33957	0.058
Mature Green Tomato/Ripe Tomato	4.49744	0.016
Immature Eggplant/Mature Eggplant	0.34891	0.064
Ripe Pepper/Ripe Tomato	1.97238	1
Mature Eggplant/Ripe Tomato	5.29211	0.268

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	0.95613
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	1.17747
6-2/M82	0.99952
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	1.79474	0.277
IL2-6/WTpooled	1.19368	0.659
IL7-5/WTpooled	1.08262	0.792
IL7-3/WTpooled	2.98673	1
IL12-4/WTpooled	1.34546	0.481
IL1-4/WTpooled	1.54922	1
WT/WTpooled	0.99069	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96758	1
DC3000/delta hrp 6h	0.94846	0.95
DC3000/delta hrp 12h	1.04532	1
DC3000/delta hrp 24h	1.04916	0.633

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	0.95141	1
Exp 36h	0.81768	0.589
Exp 60h	0.72416	0.266

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	1.23609	0.216
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.11049	0.798
transgenic ySAMdc/azygous control (breaker)	2.11353	0.172
transgenic ySAMdc/azygous control (red)	0.92897	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.52846	0.069

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.72519	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	15.0867	0.083
Manapal/WT (break)	5.62504	0.123
Manapal/WT (red)	1.3443	1