Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.8.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86258	0.303
27DAP/17DAP	1.09725	0.874
39DAP/27DAP	1.66819	0.228
41DAP/39DAP	1.16905	0.422
42DAP/41DAP	0.88728	1
43DAP/42DAP	1.03644	1
47DAP/43DAP	1.19253	0.727
52DAP/47DAP	0.82785	0.602
57DAP/52DAP	1.00692	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03057	0.814
17DAP/reference	1.12695	0.229
27DAP/reference	1.22272	0.023
39DAP/reference	1.02666	0.901
41DAP/reference	1.2416	0.021
42DAP/reference	0.93676	0.107
43DAP/reference	1.04283	0.678
47DAP/reference	1.00552	0.674
52DAP/reference	0.98163	0.53
57DAP/reference	1.00968	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9578	0.629
27DAP/17DAP	0.87977	0.537
39DAP/27DAP	1.10715	0.636
41DAP/39DAP	1.00779	1
42DAP/41DAP	0.98323	0.809
43DAP/42DAP	0.98521	0.902
47DAP/43DAP	1.02751	0.93
52DAP/47DAP	1.05594	0.804
57DAP/52DAP	0.9707	0.726
57DAP/7DAP	1.38311	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79784	0.1
17DAP/reference	1.00795	0.693
27DAP/reference	1.04987	0.371
39DAP/reference	0.93642	0.307
41DAP/reference	0.9254	0.259
42DAP/reference	1.1739	0.1
43DAP/reference	1.19997	0.2
47DAP/reference	1.12046	0.44
52DAP/reference	1.10415	0.732
57DAP/reference	0.94088	0.232

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18629	0.167
17DAP/reference	1.2031	0.034
27DAP/reference	0.98451	0.598
39DAP/reference	1.05558	0.657
41DAP/reference	1.03159	1
42DAP/reference	0.99639	0.655
43DAP/reference	1.50107	0.029
47DAP/reference	1.14582	0.105
52DAP/reference	1.04915	0.444
57DAP/reference	1.10117	0.363

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88877	0.214
17DAP/reference	1.02324	0.932
27DAP/reference	1.1475	0.179
39DAP/reference	0.88203	0.043
41DAP/reference	1.06773	0.502
42DAP/reference	0.99937	1
43DAP/reference	0.82266	0.158
47DAP/reference	1.00548	0.754
52DAP/reference	0.98726	0.763
57DAP/reference	0.9057	0.184

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08517	0.966
26DAP/20DAP	0.89196	0.205
34DAP/26DAP	1.13857	0.819
51DAP/34DAP	1.15729	0.271
52DAP/51DAP	0.84197	1
53DAP/52DAP	1.3405	0.171
55DAP/53DAP	1.2631	0.208
57DAP/55DAP	1.26411	0.955
62DAP/57DAP	1.08334	1
68DAP/62DAP	0.90104	0.7
68DAP/14DAP	1.22983	0.739

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.19112	0.496

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.67261	0.047
Immature Eggplant/Mature Eggplant	2.76449	0.05
Ripe Pepper/Ripe Tomato	0.8125	0.293
Mature Eggplant/Ripe Tomato	0.804	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01355	1
1-1-2/M82	1.00203	1
12-2/M82	N/A	N/A
12-4/M82	1.08694
1-3/M82	0.75026
2-1-1/M82	0.80018
2-1/M82	N/A	N/A
2-6/M82	0.9851
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.53327
4-3-2/M82	1.11102
4-3/M82	1.05316
5-3/M82	0.89723	0.642
6-2/M82	0.7609
6-3/M82	1.13372
7-1/M82	N/A	N/A
7-2/M82	0.85559
9-3-2/M82	1.33065

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.09785
IL2-6/WTpooled	1.13536	0.584
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.08802	1
IL12-4/WTpooled	0.8722	0.71
IL1-4/WTpooled	1.23987	1
WT/WTpooled	0.87167	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	0.95381	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08927	0.921
DC3000/delta hrp 6h	1.03008	1
DC3000/delta hrp 12h	0.9408	1
DC3000/delta hrp 24h	1.10382	0.438

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.43091	0.355
DC3000 delta B/DC3000 delta AB	1.01827	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.05227	1
Exp 60h	1.1877	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97922	1
Var 0h	1.07286	0.98
Var 12h I row2-row1	0.89082	0.627
Var 12h NI row2-row1	0.90206	0.627
Var 36h I row2-row1	0.80061	0.805
Var 36h NI row2-row1	0.95598	0.645
Var 60h I row2-row1	0.99981	1
Var 60h NI row2-row1	1.01533	1
Time course 0hI-0hNI	0.99237	1
Time course 12hI-12hNI	0.98094	0.79
Time course 36hI-36hNI	0.98291	0.533
Time course 60hI-60hNI	0.84711	0.011

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)	0.96454	0.324
transgenic ySAMdc/azygous control (breaker)	0.79247	0.142
transgenic ySAMdc/azygous control (red)	0.887	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06228	0.177

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.68856	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.0492	1
Manapal/WT (break)	0.84295	1
Manapal/WT (red)	0.82624	0.274