Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.12.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97623	0.76
27DAP/17DAP	0.94107	0.898
39DAP/27DAP	1.10643	0.816
41DAP/39DAP	0.87772	0.518
42DAP/41DAP	0.96654	1
43DAP/42DAP	0.91137	0.556
47DAP/43DAP	0.83488	0.48
52DAP/47DAP	1.22141	0.626
57DAP/52DAP	1.11554	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08853	0.814
17DAP/reference	0.71456	0.01
27DAP/reference	1.02107	0.981
39DAP/reference	0.74751	0.027
41DAP/reference	0.63885	0.01
42DAP/reference	1.12319	0.68
43DAP/reference	0.87173	0.084
47DAP/reference	1.1579	0.433
52DAP/reference	1.79342	0.024
57DAP/reference	1.39533	0.017

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02658	0.826
27DAP/17DAP	1.0553	0.826
39DAP/27DAP	0.98098	0.852
41DAP/39DAP	1.04172	1
42DAP/41DAP	1.04497	0.935
43DAP/42DAP	0.96908	0.641
47DAP/43DAP	1.00447	1
52DAP/47DAP	0.99288	0.941
57DAP/52DAP	1.12607	0.355
57DAP/7DAP	0.97934	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27378	0.047
17DAP/reference	1.23409	0.013
27DAP/reference	1.36786	0.008
39DAP/reference	1.65054	0.005
41DAP/reference	1.42984	0.016
42DAP/reference	1.66116	0.007
43DAP/reference	1.63443	0.006
47DAP/reference	1.38687	0.109
52DAP/reference	1.91776	0.007
57DAP/reference	1.92415	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81605	0.029
17DAP/reference	0.88564	0.124
27DAP/reference	1.22308	0.595
39DAP/reference	1.45957	0.377
41DAP/reference	1.93831	0.009
42DAP/reference	1.37986	0.059
43DAP/reference	0.74118	0.117
47DAP/reference	0.90697	0.105
52DAP/reference	1.11774	0.629
57DAP/reference	0.74074	0.085

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89927	0.074
17DAP/reference	1.02799	0.87
27DAP/reference	1.17625	0.081
39DAP/reference	1.34519	0.011
41DAP/reference	1.27137	0.008
42DAP/reference	1.70624	0.008
43DAP/reference	1.72071	0.013
47DAP/reference	1.15442	0.792
52DAP/reference	1.37068	0.121
57DAP/reference	2.421	0.01

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.35794	0.966
26DAP/20DAP	1.24528	0.22
34DAP/26DAP	0.96477	0.857
51DAP/34DAP	1.12488	0.261
52DAP/51DAP	0.89567	1
53DAP/52DAP	1.28596	0.033
55DAP/53DAP	0.91389	0.389
57DAP/55DAP	1.07068	0.881
62DAP/57DAP	1.14957	0.723
68DAP/62DAP	2.34393	0.305
68DAP/14DAP	7.73912	0.02

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.17176	0.151

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.61259	0.206
Mature Green Tomato/Ripe Tomato	1.087	0.948
Immature Eggplant/Mature Eggplant	1.46815	0.055
Ripe Pepper/Ripe Tomato	0.43547	0.224
Mature Eggplant/Ripe Tomato	0.5248

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.15829	0.942
12-2/M82	N/A	N/A
12-4/M82	1.14059	1
1-3/M82	1.04259
2-1-1/M82	1.32331
2-1/M82	1.37556
2-6/M82	1.40144
3-2/M82	1.01433
4-1-1/M82	N/A	N/A
4-1/M82	1.28182	0.466
4-3-2/M82	1.25394	0.508
4-3/M82	1.57689
5-3/M82	0.68003	0.395
6-2/M82	N/A	N/A
6-3/M82	1.13776	1
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.1329	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.84483	1
IL12-4/WTpooled	0.65163
IL1-4/WTpooled	1.04117	1
WT/WTpooled	1.34614	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	1.08945	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.31156	0.914
DC3000/delta hrp 6h	0.75095	0.914
DC3000/delta hrp 12h	1.08094	1
DC3000/delta hrp 24h	1.03638	0.743

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.19673	0.052
DC3000 delta B/DC3000 delta AB	1.26676	0.179

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93464	1
Exp 36h	0.8827	0.749
Exp 60h	0.97984	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9893	1
Var 0h	0.96489	1
Var 12h I row2-row1	0.97109	0.948
Var 12h NI row2-row1	1.01336	1
Var 36h I row2-row1	1.03368	1
Var 36h NI row2-row1	1.12113	1
Var 60h I row2-row1	0.85861	0.582
Var 60h NI row2-row1	1.06161	0.904
Time course 0hI-0hNI	1.00688	1
Time course 12hI-12hNI	1.02395	0.81
Time course 36hI-36hNI	1.07437	0.58
Time course 60hI-60hNI	2.47135	0.008

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)	0.99891	0.931
transgenic ySAMdc/azygous control (breaker)	0.69843	0.15
transgenic ySAMdc/azygous control (red)	1.108	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.29426	0.034

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.05671	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.94266	1
Manapal/WT (break)	1.0663	1
Manapal/WT (red)	0.55806	0.242