Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.14.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95515	0.699
27DAP/17DAP	1.18676	0.819
39DAP/27DAP	1.83502	0.035
41DAP/39DAP	0.63993	0.068
42DAP/41DAP	1.38811	0.802
43DAP/42DAP	1.16352	1
47DAP/43DAP	1.11675	0.979
52DAP/47DAP	1.02281	0.873
57DAP/52DAP	1.34113	0.859

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83443	0.159
17DAP/reference	0.64353	0.009
27DAP/reference	1.04828	0.925
39DAP/reference	0.93284	0.437
41DAP/reference	0.73417	0.014
42DAP/reference	1.04093	0.869
43DAP/reference	1.18487	0.064
47DAP/reference	1.29387	0.021
52DAP/reference	1.65407	0.008
57DAP/reference	1.8692	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9338	0.509
27DAP/17DAP	1.11193	0.706
39DAP/27DAP	1.09291	0.499
41DAP/39DAP	0.89536	0.729
42DAP/41DAP	1.04333	0.976
43DAP/42DAP	1.18386	0.02
47DAP/43DAP	1.20072	0.593
52DAP/47DAP	1.00875	0.986
57DAP/52DAP	1.1313	0.421
57DAP/7DAP	1.23946	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1188	0.338
17DAP/reference	0.95286	0.192
27DAP/reference	0.98891	0.571
39DAP/reference	1.18475	0.028
41DAP/reference	1.18232	0.08
42DAP/reference	1.17079	0.174
43DAP/reference	1.46966	0.006
47DAP/reference	1.501	0.019
52DAP/reference	1.21948	0.036
57DAP/reference	1.2245	0.082

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.711	0.012
17DAP/reference	0.61227	0.006
27DAP/reference	0.95479	0.423
39DAP/reference	1.31561	0.182
41DAP/reference	1.86668	0.005
42DAP/reference	1.45436	0.007
43DAP/reference	0.69285	0.039
47DAP/reference	1.44791	0.008
52DAP/reference	1.16083	0.24
57DAP/reference	0.85363	0.194

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84223	0.074
17DAP/reference	0.85442	0.239
27DAP/reference	1.06147	0.26
39DAP/reference	1.10037	0.157
41DAP/reference	0.97272	0.459
42DAP/reference	1.51242	0.027
43DAP/reference	1.43812	0.035
47DAP/reference	1.36755	0.196
52DAP/reference	1.42139	0.031
57DAP/reference	3.65593	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05683	0.966
26DAP/20DAP	1.22253	0.453
34DAP/26DAP	0.86419	0.675
51DAP/34DAP	1.20098	0.084
52DAP/51DAP	0.75054	1
53DAP/52DAP	1.21651	0.121
55DAP/53DAP	0.87086	0.159
57DAP/55DAP	1.24111	0.955
62DAP/57DAP	0.87233	0.466
68DAP/62DAP	2.37775	0.23
68DAP/14DAP	3.49439	0.019

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.04846	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.82672	0.282
Mature Green Tomato/Ripe Tomato	0.62424	0.02
Immature Eggplant/Mature Eggplant	1.17838	0.069
Ripe Pepper/Ripe Tomato	1.05874	1
Mature Eggplant/Ripe Tomato	0.93684	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.14298	0.443
1-1-2/M82	1.1008	0.977
12-2/M82	1.05103	1
12-4/M82	1.23546	1
1-3/M82	1.75936	0.26
2-1-1/M82	1.0737	1
2-1/M82	0.9424	1
2-6/M82	1.11502	0.695
3-2/M82	0.99467	1
4-1-1/M82	1.12911	1
4-1/M82	1.27743	1
4-3-2/M82	1.19881	0.284
4-3/M82	1.20849	1
5-3/M82	1.18994
6-2/M82	1.14879	1
6-3/M82	1.04428	1
7-1/M82	1.0739	1
7-2/M82	1.26568	0.324
9-3-2/M82	1.44472	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.89773	0.321
IL2-6/WTpooled	1.01648	1
IL7-5/WTpooled	1.02108	1
IL7-3/WTpooled	0.9087
IL12-4/WTpooled	1.1857	0.891
IL1-4/WTpooled	0.88719	0.834
WT/WTpooled	1.05453	0.999

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	1.17063	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94932	0.839
DC3000/delta hrp 6h	1.10139	0.978
DC3000/delta hrp 12h	1.13049	1
DC3000/delta hrp 24h	0.9094	0.33

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.20804	0.042
DC3000 delta B/DC3000 delta AB	1.20932	0.164

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.11168	1
Exp 36h	0.96899	0.943
Exp 60h	1.00028	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98971	1
Var 0h	0.56337	0.263
Var 12h I row2-row1	1.03606	0.58
Var 12h NI row2-row1	1.08753	1
Var 36h I row2-row1	1.21589	0.489
Var 36h NI row2-row1	0.98654	0.852
Var 60h I row2-row1	0.85147	0.832
Var 60h NI row2-row1	0.86835	0.572
Time course 0hI-0hNI	1.03814	0.852
Time course 12hI-12hNI	0.95201	0.745
Time course 36hI-36hNI	1.06714	0.07
Time course 60hI-60hNI	1.0578	0.426

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)	1.05661	0.571
transgenic ySAMdc/azygous control (breaker)	0.63124	0.131
transgenic ySAMdc/azygous control (red)	0.95381	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.21894	0.089

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.04709	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.97912	1
Manapal/WT (break)	1.05099	1
Manapal/WT (red)	0.67647	0.181