Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.13.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94079	0.683
27DAP/17DAP	1.21266	0.809
39DAP/27DAP	0.82645	0.529
41DAP/39DAP	1.0529	0.978
42DAP/41DAP	0.94755	1
43DAP/42DAP	1.08515	1
47DAP/43DAP	1.4054	0.412
52DAP/47DAP	0.92541	0.724
57DAP/52DAP	1.26113	0.853

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03547	0.685
17DAP/reference	1.11656	0.089
27DAP/reference	1.00937	1
39DAP/reference	1.03864	0.453
41DAP/reference	1.07395	0.241
42DAP/reference	0.92204	0.059
43DAP/reference	0.90888	0.36
47DAP/reference	0.93233	0.032
52DAP/reference	0.86483	0.027
57DAP/reference	0.98302	0.553

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80455	0.402
27DAP/17DAP	0.96756	0.887
39DAP/27DAP	1.05758	0.532
41DAP/39DAP	1.0909	0.868
42DAP/41DAP	0.9606	0.737
43DAP/42DAP	1.11122	0.413
47DAP/43DAP	1.05181	0.906
52DAP/47DAP	1.01355	0.962
57DAP/52DAP	1.06871	0.864
57DAP/7DAP	0.99289	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86629	0.168
17DAP/reference	0.82437	0.024
27DAP/reference	0.78557	0.042
39DAP/reference	0.97418	0.474
41DAP/reference	0.98515	0.589
42DAP/reference	0.88439	0.031
43DAP/reference	0.88638	0.166
47DAP/reference	0.83949	0.066
52DAP/reference	0.77651	0.017
57DAP/reference	0.81094	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92992	0.238
17DAP/reference	0.93758	0.307
27DAP/reference	0.88415	0.071
39DAP/reference	0.93156	0.306
41DAP/reference	0.82723	0.047
42DAP/reference	0.87762	0.108
43DAP/reference	1.02208	0.939
47DAP/reference	1.033	0.388
52DAP/reference	0.87322	0.016
57DAP/reference	1.0191	0.93

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8833	0.158
17DAP/reference	0.93792	0.364
27DAP/reference	0.85432	0.053
39DAP/reference	0.83456	0.018
41DAP/reference	0.85736	0.025
42DAP/reference	0.77017	0.032
43DAP/reference	0.74752	0.039
47DAP/reference	0.91175	0.191
52DAP/reference	0.88725	0.351
57DAP/reference	0.6829	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.80141	0.585
26DAP/20DAP	0.6905	0.317
34DAP/26DAP	1.45	0.819
51DAP/34DAP	0.95069	0.66
52DAP/51DAP	0.97049	1
53DAP/52DAP	1.07993	0.858
55DAP/53DAP	0.9554	0.725
57DAP/55DAP	1.11421	0.745
62DAP/57DAP	0.9863	0.994
68DAP/62DAP	1.0284	1
68DAP/14DAP	0.88888	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.8524	0.076

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.05887	0.898
Immature Eggplant/Mature Eggplant	0.923
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.74688
12-2/M82	N/A	N/A
12-4/M82	0.40841
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	0.8099
3-2/M82	1.03534
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	0.91998	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	0.72547	0.243
IL2-6/WTpooled	0.8444	0.473
IL7-5/WTpooled	0.31229	1
IL7-3/WTpooled	0.94934	1
IL12-4/WTpooled	0.84486	0.581
IL1-4/WTpooled	0.95208	1
WT/WTpooled	0.99946	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	0.89474	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04644	0.921
DC3000/delta hrp 6h	0.53921
DC3000/delta hrp 12h	1.07254	1
DC3000/delta hrp 24h	1.17217	0.356

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	0.39737

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	2.13231	1
Exp 36h	0.94058	0.943
Exp 60h	1.09588	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.41324	1
Var 0h	1.05921	0.782
Var 12h I row2-row1	0.52401	1
Var 12h NI row2-row1	1.00933
Var 36h I row2-row1	0.2956	1
Var 36h NI row2-row1	0.91298	0.791
Var 60h I row2-row1	0.98435	0.832
Var 60h NI row2-row1	0.93532	0.292
Time course 0hI-0hNI	1.08675	0.574
Time course 12hI-12hNI	0.85788	0.906
Time course 36hI-36hNI	1.4319	0.218
Time course 60hI-60hNI	1.2323	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)	0.89434	0.3
transgenic ySAMdc/azygous control (breaker)	0.88776	0.251
transgenic ySAMdc/azygous control (red)	1.04083	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94777	0.051

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.99773	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.84695	0.172
Manapal/WT (break)	0.82701	0.333
Manapal/WT (red)	0.84469	0.424