Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.3.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84231	0.217
27DAP/17DAP	0.91274	0.81
39DAP/27DAP	0.94484	0.652
41DAP/39DAP	1.04429	0.978
42DAP/41DAP	0.92078	1
43DAP/42DAP	0.99085	0.937
47DAP/43DAP	1.04082	0.965
52DAP/47DAP	1.31437	0.575
57DAP/52DAP	0.82696	0.613

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01347	1
17DAP/reference	1.02341	0.492
27DAP/reference	0.96384	0.275
39DAP/reference	1.02104	0.691
41DAP/reference	1.03045	0.759
42DAP/reference	0.99183	0.484
43DAP/reference	1.08486	0.34
47DAP/reference	0.93645	0.077
52DAP/reference	0.90228	0.073
57DAP/reference	0.96427	0.235

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97436	0.697
27DAP/17DAP	1.12351	0.794
39DAP/27DAP	0.96521	0.692
41DAP/39DAP	1.07697	0.914
42DAP/41DAP	1.09143	0.675
43DAP/42DAP	1.00696	1
47DAP/43DAP	1.05481	0.906
52DAP/47DAP	0.92435	0.71
57DAP/52DAP	0.90003	0.507
57DAP/7DAP	0.94472	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82729	0.049
17DAP/reference	0.90867	0.144
27DAP/reference	0.86451	0.094
39DAP/reference	0.82297	0.031
41DAP/reference	0.81584	0.021
42DAP/reference	0.84858	0.035
43DAP/reference	0.71127	0.02
47DAP/reference	0.87442	0.168
52DAP/reference	0.68954	0.012
57DAP/reference	0.89417	0.199

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97644	0.706
17DAP/reference	1.04904	0.584
27DAP/reference	1.02905	0.875
39DAP/reference	0.9571	0.314
41DAP/reference	0.92397	0.205
42DAP/reference	0.95767	0.289
43DAP/reference	1.21848	0.058
47DAP/reference	1.08846	0.256
52DAP/reference	1.15697	0.012
57DAP/reference	1.19424	0.236

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89586	0.119
17DAP/reference	0.95564	0.477
27DAP/reference	0.9655	0.133
39DAP/reference	0.87178	0.054
41DAP/reference	0.96951	0.56
42DAP/reference	0.96557	0.552
43DAP/reference	0.87769	0.047
47DAP/reference	1.01187	1
52DAP/reference	1.01842	0.917
57DAP/reference	0.738	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99058	1
26DAP/20DAP	0.87432	0.512
34DAP/26DAP	0.90532	0.519
51DAP/34DAP	0.98786	0.883
52DAP/51DAP	1.05383	0.86
53DAP/52DAP	0.99234	0.978
55DAP/53DAP	1.10237	0.608
57DAP/55DAP	0.98736	0.923
62DAP/57DAP	1.54576	0.35
68DAP/62DAP	1.14609	0.89
68DAP/14DAP	0.97543	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.26612	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.55836
Mature Green Tomato/Ripe Tomato	0.92898	0.256
Immature Eggplant/Mature Eggplant	0.90387	0.254
Ripe Pepper/Ripe Tomato	0.37513	0.224
Mature Eggplant/Ripe Tomato	1.3392	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01954	1
1-1-2/M82	1.02848
12-2/M82	1.10782
12-4/M82	0.86438	0.619
1-3/M82	0.63496	0.441
2-1-1/M82	1.22729	0.343
2-1/M82	N/A	N/A
2-6/M82	1.0231	1
3-2/M82	0.81042
4-1-1/M82	0.96605	1
4-1/M82	1.45888
4-3-2/M82	0.96989	1
4-3/M82	1.00857	1
5-3/M82	1.04154	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.02992	1
7-2/M82	0.88512	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.58809	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.0442	0.792
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.99607	1
WT/WTpooled	N/A	N/A

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	1.03528	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02204	0.921
DC3000/delta hrp 6h	0.92061	0.95
DC3000/delta hrp 12h	1.0919	1
DC3000/delta hrp 24h	1.08868	0.422

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.88537
DC3000 delta B/DC3000 delta AB	1.13254	0.403

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01655	1
Exp 36h	0.88817	0.749
Exp 60h	1.01536	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95788	1
Var 0h	1.26914	0.289
Var 12h I row2-row1	1.13082	0.263
Var 12h NI row2-row1	0.95449	0.82
Var 36h I row2-row1	1.05013	1
Var 36h NI row2-row1	1.12404	1
Var 60h I row2-row1	1.4072	0.562
Var 60h NI row2-row1	0.99281	1
Time course 0hI-0hNI	1.05385	0.574
Time course 12hI-12hNI	1.01624	0.849
Time course 36hI-36hNI	1.20379	0.006
Time course 60hI-60hNI	1.28899	0.01

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)	0.8825	0.33
transgenic ySAMdc/azygous control (breaker)	1.06696	1
transgenic ySAMdc/azygous control (red)	1.00068	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03551	0.059

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.38946	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.13069	0.105
Manapal/WT (break)	0.83784	0.333
Manapal/WT (red)	0.88877	0.181