Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.11.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08875	0.545
27DAP/17DAP	1.05351	0.9
39DAP/27DAP	0.9096	0.549
41DAP/39DAP	1.47636	0.265
42DAP/41DAP	0.953	1
43DAP/42DAP	0.94921	0.877
47DAP/43DAP	0.85528	0.54
52DAP/47DAP	0.96905	0.851
57DAP/52DAP	1.14262	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93758	0.145
17DAP/reference	1.06491	0.369
27DAP/reference	0.97603	0.567
39DAP/reference	0.96861	0.611
41DAP/reference	0.99423	0.814
42DAP/reference	0.92705	0.043
43DAP/reference	1.01095	0.866
47DAP/reference	0.93299	0.071
52DAP/reference	0.92385	0.183
57DAP/reference	1.01939	0.876

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99009	0.782
27DAP/17DAP	0.96459	0.58
39DAP/27DAP	1.03517	0.636
41DAP/39DAP	1.03275	0.837
42DAP/41DAP	0.97555	0.753
43DAP/42DAP	1.02189	0.585
47DAP/43DAP	1.00953	0.941
52DAP/47DAP	0.9783	0.907
57DAP/52DAP	1.0337	0.825
57DAP/7DAP	1.05975	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87551	0.074
17DAP/reference	0.96607	0.192
27DAP/reference	0.94617	0.066
39DAP/reference	0.94156	0.049
41DAP/reference	0.99799	0.778
42DAP/reference	0.94065	0.178
43DAP/reference	0.91385	0.047
47DAP/reference	0.83566	0.038
52DAP/reference	0.91302	0.04
57DAP/reference	0.93105	0.038

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94218	0.386
17DAP/reference	0.93079	0.08
27DAP/reference	0.88402	0.115
39DAP/reference	0.9541	0.281
41DAP/reference	0.90055	0.1
42DAP/reference	0.94139	0.261
43DAP/reference	0.98099	0.607
47DAP/reference	1.04631	0.264
52DAP/reference	0.9423	0.093
57DAP/reference	0.96591	0.384

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89849	0.074
17DAP/reference	0.96288	0.342
27DAP/reference	0.95611	0.184
39DAP/reference	0.94946	0.037
41DAP/reference	0.90992	0.096
42DAP/reference	0.83167	0.071
43DAP/reference	0.93313	0.305
47DAP/reference	0.95465	0.396
52DAP/reference	0.96728	0.582
57DAP/reference	0.77761	0.018

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03723	0.752
26DAP/20DAP	1.00669	1
34DAP/26DAP	1.07765	0.542
51DAP/34DAP	0.98069	0.856
52DAP/51DAP	0.97692	1
53DAP/52DAP	0.96415	0.807
55DAP/53DAP	0.92959	0.336
57DAP/55DAP	1.03156	1
62DAP/57DAP	1.074	0.515
68DAP/62DAP	0.99575	0.885
68DAP/14DAP	1.35	0.346

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.89702	0.129

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.09604	1
Mature Green Tomato/Ripe Tomato	0.88556	0.411
Immature Eggplant/Mature Eggplant	1.07569	0.507
Ripe Pepper/Ripe Tomato	2.38323
Mature Eggplant/Ripe Tomato	2.44168

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04495	1
1-1-2/M82	0.99282	1
12-2/M82	0.96044	0.955
12-4/M82	0.98735	1
1-3/M82	0.98718	1
2-1-1/M82	1.16374	0.764
2-1/M82	1.50747	1
2-6/M82	0.91547	1
3-2/M82	1.06081	0.84
4-1-1/M82	1.00682	1
4-1/M82	0.87004	1
4-3-2/M82	1.13714	0.508
4-3/M82	1.04468	1
5-3/M82	1.00745	1
6-2/M82	1.14724	0.219
6-3/M82	1.00126	1
7-1/M82	1.02168	1
7-2/M82	1.07931	1
9-3-2/M82	0.88831	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.98284	1
IL2-6/WTpooled	0.82373	0.348
IL7-5/WTpooled	0.81829	1
IL7-3/WTpooled	1.14501	0.362
IL12-4/WTpooled	1.00929	1
IL1-4/WTpooled	1.04242	1
WT/WTpooled	1.04834	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	1.06149	0.914
DC3000/delta hrp 6h	1.19708	0.95
DC3000/delta hrp 12h	0.95473	1
DC3000/delta hrp 24h	1.02081	0.76

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.02101	0.515
DC3000 delta B/DC3000 delta AB	1.02726	0.614

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98748	1
Var 0h	1.17229	0.98
Var 12h I row2-row1	1.1206	0.348
Var 12h NI row2-row1	0.95263	0.82
Var 36h I row2-row1	0.97582	1
Var 36h NI row2-row1	0.84598	0.478
Var 60h I row2-row1	1.29777	0.562
Var 60h NI row2-row1	1.13625	0.904
Time course 0hI-0hNI	1.14735	0.764
Time course 12hI-12hNI	1.06506	0.698
Time course 36hI-36hNI	1.0087	1
Time course 60hI-60hNI	1.19508	0.011

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)	0.76375	0.529
transgenic ySAMdc/azygous control (breaker)	1.56559	0.248
transgenic ySAMdc/azygous control (red)	1.39319	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93598	0.181

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.06812	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.278	1
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.84406	0.274