Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.4.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.63003	0.026
27DAP/17DAP	1.01244	1
39DAP/27DAP	0.75285	0.39
41DAP/39DAP	1.71372	0.243
42DAP/41DAP	1.07458	1
43DAP/42DAP	1.05829	1
47DAP/43DAP	0.95413	0.804
52DAP/47DAP	1.69911	0.403
57DAP/52DAP	0.98799	0.982

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0524	0.384
17DAP/reference	1.00973	0.874
27DAP/reference	1.029	0.58
39DAP/reference	0.99441	0.855
41DAP/reference	1.10879	0.265
42DAP/reference	0.92944	0.081
43DAP/reference	1.04032	0.233
47DAP/reference	0.93393	0.077
52DAP/reference	0.99217	0.636
57DAP/reference	0.90149	0.042

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90636	0.185
27DAP/17DAP	0.99024	0.943
39DAP/27DAP	1.04458	0.558
41DAP/39DAP	1.0716	0.79
42DAP/41DAP	1.01412	0.947
43DAP/42DAP	0.99535	1
47DAP/43DAP	1.0118	0.93
52DAP/47DAP	0.99661	0.969
57DAP/52DAP	1.00391	1
57DAP/7DAP	1.17738	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91062	0.122
17DAP/reference	0.90688	0.011
27DAP/reference	0.90874	0.01
39DAP/reference	0.9561	0.064
41DAP/reference	0.90422	0.018
42DAP/reference	0.93789	0.03
43DAP/reference	0.8889	0.012
47DAP/reference	0.88097	0.066
52DAP/reference	0.89148	0.014
57DAP/reference	0.89053	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14631	0.043
17DAP/reference	1.10495	0.081
27DAP/reference	0.95961	0.393
39DAP/reference	0.99608	0.682
41DAP/reference	0.92528	0.205
42DAP/reference	0.94706	0.169
43DAP/reference	0.96686	0.539
47DAP/reference	0.97551	0.261
52DAP/reference	0.91198	0.302
57DAP/reference	1.02502	0.868

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02651	0.918
17DAP/reference	1.05993	0.602
27DAP/reference	0.93332	0.044
39DAP/reference	0.91326	0.054
41DAP/reference	1.00282	1
42DAP/reference	0.92086	0.049
43DAP/reference	0.88157	0.033
47DAP/reference	0.94534	0.132
52DAP/reference	0.85485	0.114
57DAP/reference	0.95355	0.41

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03601	0.966
26DAP/20DAP	0.92736	1
34DAP/26DAP	0.96099	0.861
51DAP/34DAP	0.9233	0.213
52DAP/51DAP	0.99439	1
53DAP/52DAP	0.96358	0.817
55DAP/53DAP	0.97962	0.784
57DAP/55DAP	1.07334	0.915
62DAP/57DAP	1.53361	0.678
68DAP/62DAP	0.93424	0.787
68DAP/14DAP	0.9676	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.9817	0.52

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.25586	0.267
Immature Eggplant/Mature Eggplant	1.8996	0.05
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	9.1674	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0242	1
1-1-2/M82	1.02922
12-2/M82	0.96817	1
12-4/M82	0.92987	1
1-3/M82	0.72586
2-1-1/M82	1.19216
2-1/M82	0.94216
2-6/M82	1.12659	0.695
3-2/M82	0.7386
4-1-1/M82	N/A	N/A
4-1/M82	0.88614	1
4-3-2/M82	0.84251	0.698
4-3/M82	0.59743
5-3/M82	0.99127	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.8721
7-2/M82	0.99292
9-3-2/M82	1.07649

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.03837	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.02514	1
IL12-4/WTpooled	0.94671	0.581
IL1-4/WTpooled	0.88881
WT/WTpooled	1.04542	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	0.85541	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0129	0.921
DC3000/delta hrp 6h	0.88081	0.95
DC3000/delta hrp 12h	0.91028	1
DC3000/delta hrp 24h	1.12166	0.438

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.00876	0.648
DC3000 delta B/DC3000 delta AB	0.97188	0.729

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.80431	1
Exp 36h	1.32627	1
Exp 60h	0.91527	0.754

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	0.93451	1
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)	1.45342	0.23
transgenic ySAMdc/azygous control (breaker)	1.84754	0.178
transgenic ySAMdc/azygous control (red)	1.13026	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0206	0.587

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.62472	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.98463	1
Manapal/WT (break)	0.78488	1
Manapal/WT (red)	0.56393	0.187