Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.2.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.67209	0.137
27DAP/17DAP	0.81042	0.478
39DAP/27DAP	1.19734	0.885
41DAP/39DAP	1.33627	0.323
42DAP/41DAP	0.54055	0.262
43DAP/42DAP	0.70991	0.454
47DAP/43DAP	0.80082	0.407
52DAP/47DAP	1.41968	0.566
57DAP/52DAP	0.91585	0.919

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06565	0.587
17DAP/reference	1.08628	0.27
27DAP/reference	0.90789	0.286
39DAP/reference	0.92992	0.24
41DAP/reference	1.01636	1
42DAP/reference	0.98884	0.531
43DAP/reference	0.98597	0.84
47DAP/reference	0.89107	0.071
52DAP/reference	1.05355	0.991
57DAP/reference	1.14434

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.55269	0.068
27DAP/17DAP	1.6645	0.035
39DAP/27DAP	0.68098	0.126
41DAP/39DAP	1.79478	0.025
42DAP/41DAP	0.6891	0.091
43DAP/42DAP	1.40641	0.052
47DAP/43DAP	1.33096	0.108
52DAP/47DAP	1.1395	0.789
57DAP/52DAP	2.53089	0.029
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.33315	0.075
17DAP/reference	1.17358	0.014
27DAP/reference	1.16369	0.107
39DAP/reference	1.10577	0.865
41DAP/reference	1.03817	0.655
42DAP/reference	0.9376	0.393
43DAP/reference	1.07414	0.974
47DAP/reference	1.14798	0.901
52DAP/reference	1.09476	0.732
57DAP/reference	1.03085	0.694

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06415	0.933
17DAP/reference	1.02912	0.658
27DAP/reference	0.93116	0.381
39DAP/reference	0.97804	0.526
41DAP/reference	0.99565	0.649
42DAP/reference	0.86112	0.15
43DAP/reference	0.84419	0.077
47DAP/reference	0.86361	0.023
52DAP/reference	0.96215	0.433
57DAP/reference	0.95413	0.408

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31594	0.103
17DAP/reference	1.26714	0.365
27DAP/reference	0.87141
39DAP/reference	0.96277	0.693
41DAP/reference	1.04217	0.984
42DAP/reference	0.87421	0.134
43DAP/reference	0.88095	0.237
47DAP/reference	0.97001	0.509
52DAP/reference	1.10207	0.457
57DAP/reference	1.06609	0.717

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.47078	0.85
26DAP/20DAP	1.74369	0.103
34DAP/26DAP	0.70068	0.311
51DAP/34DAP	0.69647	0.121
52DAP/51DAP	1.17186	0.925
53DAP/52DAP	1.31745	0.552
55DAP/53DAP	1.04023	0.951
57DAP/55DAP	1.02438	0.975
62DAP/57DAP	1.45682	0.569
68DAP/62DAP	1.298	0.353
68DAP/14DAP	0.96315	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.7218	0.131

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	5.03684	0.089
Mature Green Tomato/Ripe Tomato	1.00102	0.835
Immature Eggplant/Mature Eggplant	0.54271	0.062
Ripe Pepper/Ripe Tomato	0.56708	1
Mature Eggplant/Ripe Tomato	1.90661	1

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	0.73124
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	N/A	N/A
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	1.03004	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.97836	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.05525	1
IL12-4/WTpooled	1.08185	0.839
IL1-4/WTpooled	1.02436
WT/WTpooled	1.13008	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	0.89615	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04424	0.921
DC3000/delta hrp 6h	0.71645	0.942
DC3000/delta hrp 12h	0.85823	1
DC3000/delta hrp 24h	1.33163	0.069

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.03411	0.598
DC3000 delta B/DC3000 delta AB	0.86155	0.445

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.80493	1
Exp 36h	1.05291	1
Exp 60h	0.78223	0.278

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04809	1
Var 0h	0.80651	1
Var 12h I row2-row1	0.90371	0.705
Var 12h NI row2-row1	1.32611	0.235
Var 36h I row2-row1	0.99053	1
Var 36h NI row2-row1	1.2313	1
Var 60h I row2-row1	0.90962	0.832
Var 60h NI row2-row1	1.14948	0.904
Time course 0hI-0hNI	1.10106	0.852
Time course 12hI-12hNI	0.8574	0.14
Time course 36hI-36hNI	0.83584	0.142
Time course 60hI-60hNI	0.54359	0.006

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)	1.28406	0.397
transgenic ySAMdc/azygous control (breaker)	0.69634	0.15
transgenic ySAMdc/azygous control (red)	1.25523	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02744	0.185

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.63721	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.07881	1
Manapal/WT (break)	1.08728	1
Manapal/WT (red)	1.0307	0.863