Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.10.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00895	0.975
27DAP/17DAP	1.05	1
39DAP/27DAP	1.05865	0.922
41DAP/39DAP	1.49435	0.114
42DAP/41DAP	1.43207	0.871
43DAP/42DAP	0.8065	0.495
47DAP/43DAP	1.33368	0.68
52DAP/47DAP	1.4997	0.545
57DAP/52DAP	0.70336	0.462

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00549	1
17DAP/reference	1.00192	1
27DAP/reference	1.00007	0.885
39DAP/reference	1.06506	0.236
41DAP/reference	1.03844	0.714
42DAP/reference	1.02648	0.706
43DAP/reference	1.09407	0.102
47DAP/reference	0.86106	0.055
52DAP/reference	0.78713	0.131
57DAP/reference	0.77228	0.017

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89975	0.402
27DAP/17DAP	1.06479	0.98
39DAP/27DAP	1.04993	0.698
41DAP/39DAP	1.17492	0.895
42DAP/41DAP	1.10867	0.773
43DAP/42DAP	1.02942	0.788
47DAP/43DAP	1.06174	0.833
52DAP/47DAP	0.98951	0.93
57DAP/52DAP	1.08865	0.622
57DAP/7DAP	1.62315	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93774	0.138
17DAP/reference	0.91291	0.049
27DAP/reference	0.88932	0.011
39DAP/reference	0.86028	0.013
41DAP/reference	0.88707	0.025
42DAP/reference	0.86062	0.014
43DAP/reference	0.87923	0.016
47DAP/reference	0.8973	0.168
52DAP/reference	0.85051	0.053
57DAP/reference	0.78606	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13988	0.201
17DAP/reference	1.04817	0.824
27DAP/reference	0.87559	0.269
39DAP/reference	0.88724	0.235
41DAP/reference	0.84348	0.085
42DAP/reference	0.95447	0.433
43DAP/reference	1.17538	0.293
47DAP/reference	1.11526	0.256
52DAP/reference	1.00339	0.761
57DAP/reference	1.4541	0.034

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92392	0.311
17DAP/reference	1.0439	0.833
27DAP/reference	0.83975	0.033
39DAP/reference	0.85653	0.037
41DAP/reference	0.82102	0.027
42DAP/reference	0.77617	0.134
43DAP/reference	0.72441	0.092
47DAP/reference	1.00417	0.646
52DAP/reference	0.99947	0.871
57DAP/reference	0.58638	0.021

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.11439	0.945
26DAP/20DAP	0.7776	0.244
34DAP/26DAP	1.14335	0.542
51DAP/34DAP	0.82549	0.094
52DAP/51DAP	1.0317	0.783
53DAP/52DAP	1.13004	0.643
55DAP/53DAP	1.18782	0.361
57DAP/55DAP	1.02229	0.986
62DAP/57DAP	1.24143	0.303
68DAP/62DAP	0.82541	0.314
68DAP/14DAP	0.75884	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.82648	0.186

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.10003	1
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	10.7581
Mature Eggplant/Ripe Tomato	1.32404	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.87423	0.605
1-1-2/M82	0.87679	1
12-2/M82	1.14193	1
12-4/M82	1.03985	1
1-3/M82	0.85298	0.501
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.05249	1
3-2/M82	1.04736
4-1-1/M82	1.03648	1
4-1/M82	0.68632	0.715
4-3-2/M82	1.00037
4-3/M82	0.90194	0.72
5-3/M82	0.98825	1
6-2/M82	0.94298	1
6-3/M82	0.92801	1
7-1/M82	1.03364
7-2/M82	0.90864	0.796
9-3-2/M82	0.57887

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.23203	0.277
IL2-6/WTpooled	0.45524	0.473
IL7-5/WTpooled	0.96423	1
IL7-3/WTpooled	0.79056	0.31
IL12-4/WTpooled	1.11185	0.891
IL1-4/WTpooled	0.79777	0.444
WT/WTpooled	0.88536	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	1.07997	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05163	0.921
DC3000/delta hrp 6h	0.96047	0.95
DC3000/delta hrp 12h	1.23392	1
DC3000/delta hrp 24h	1.05878	0.604

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	0.88053	0.21

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	0.91226	1
Var 0h	0.74205	0.594
Var 12h I row2-row1	1.05506	0.506
Var 12h NI row2-row1	0.91536	0.713
Var 36h I row2-row1	0.84252	0.438
Var 36h NI row2-row1	1.01902	1
Var 60h I row2-row1	1.72498	0.562
Var 60h NI row2-row1	1.29013	0.904
Time course 0hI-0hNI	1.17478	0.603
Time course 12hI-12hNI	1.04404	0.779
Time course 36hI-36hNI	0.99596	0.753
Time course 60hI-60hNI	1.10344	0.187

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)	0.92713	0.33
transgenic ySAMdc/azygous control (breaker)	1.1382	1
transgenic ySAMdc/azygous control (red)	1.27407	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00695	0.958

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.08525	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.95212	1
Manapal/WT (break)	1.39323	0.381
Manapal/WT (red)	1.52356	0.222