Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.4.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9734	0.788
27DAP/17DAP	1.30853	0.793
39DAP/27DAP	1.24356	0.685
41DAP/39DAP	0.65312	0.153
42DAP/41DAP	1.17646	0.876
43DAP/42DAP	1.06861	1
47DAP/43DAP	0.92795	0.729
52DAP/47DAP	0.86649	0.662
57DAP/52DAP	0.61625	0.591

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87077	0.182
17DAP/reference	0.91592	0.194
27DAP/reference	1.14969	0.125
39DAP/reference	1.1048	0.486
41DAP/reference	0.83345	0.039
42DAP/reference	2.4562	0.001
43DAP/reference	1.30982	0.009
47DAP/reference	2.56154	0.006
52DAP/reference	1.94496	0.008
57DAP/reference	1.40398	0.063

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.35464	0.048
27DAP/17DAP	0.71315	0.172
39DAP/27DAP	1.16215	0.615
41DAP/39DAP	0.88972	0.822
42DAP/41DAP	0.82545	0.164
43DAP/42DAP	0.89494	0.482
47DAP/43DAP	1.43037	0.024
52DAP/47DAP	1.08292	0.919
57DAP/52DAP	0.9777	0.753
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.22515	0.028
17DAP/reference	5.30646	0.006
27DAP/reference	4.92356	0.006
39DAP/reference	6.9175	0.005
41DAP/reference	7.48131	0.012
42DAP/reference	8.55109	0.006
43DAP/reference	9.91524	0.006
47DAP/reference	4.63411	0.045
52DAP/reference	7.07078	0.007
57DAP/reference	7.11954	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02817	0.951
17DAP/reference	0.82754	0.23
27DAP/reference	0.92475	0.173
39DAP/reference	0.88595	0.077
41DAP/reference	1.19495	0.057
42DAP/reference	1.03313	0.759
43DAP/reference	0.78468	0.212
47DAP/reference	0.85037	0.02
52DAP/reference	1.25576	0.559
57DAP/reference	0.89128	0.169

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.68359	0.062
17DAP/reference	1.96633	0.298
27DAP/reference	3.86786	0.023
39DAP/reference	3.81134	0.021
41DAP/reference	4.31344	0.006
42DAP/reference	4.6804	0.011
43DAP/reference	5.08834	0.007
47DAP/reference	1.60969	0.007
52DAP/reference	5.54557	0.074
57DAP/reference	3.30318	0.068

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.22766	0.966
26DAP/20DAP	1.29904	0.319
34DAP/26DAP	N/A	N/A
51DAP/34DAP	0.95241
52DAP/51DAP	N/A	N/A
53DAP/52DAP	1.13788	0.678
55DAP/53DAP	N/A	N/A
57DAP/55DAP	0.76926	0.437
62DAP/57DAP	0.91452
68DAP/62DAP	1.64871	0.013
68DAP/14DAP	0.87117	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02116	0.821

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.8057	0.364
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.46643	0.293
Mature Eggplant/Ripe Tomato	0.34182

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	N/A	N/A
3-2/M82	N/A	N/A
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	0.95033
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	0.9492	1
IL2-6/WTpooled	0.85856
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.89186	0.562
WT/WTpooled	1.24714

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04943	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.89527	1
DC3000/delta hrp 24h	0.57187	0.034

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	N/A	N/A

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	N/A	N/A
Var 0h	1.817
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.09325	0.511
transgenic ySAMdc/azygous control (breaker)	2.59269	0.172
transgenic ySAMdc/azygous control (red)	1.32723	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02087	0.471

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.99671	0.14
Manapal/WT (break)	1.31035	0.381
Manapal/WT (red)	1.86819	0.142