Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-1.2.12.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.55296	0.014
27DAP/17DAP	1.1956	0.833
39DAP/27DAP	1.25423	0.691
41DAP/39DAP	0.92349	0.67
42DAP/41DAP	0.82401	0.774
43DAP/42DAP	0.87512	0.765
47DAP/43DAP	1.09347	0.809
52DAP/47DAP	1.41569	0.269
57DAP/52DAP	0.93397	0.92

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23972	0.093
17DAP/reference	1.52213	0.049
27DAP/reference	1.24781	0.056
39DAP/reference	0.8855	0.36
41DAP/reference	1.00893	1
42DAP/reference	1.05773	1
43DAP/reference	0.8591	0.259
47DAP/reference	1.11423	0.318
52DAP/reference	0.88817	0.319
57DAP/reference	1.06844	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.77393	0.158
27DAP/17DAP	1.03566	1
39DAP/27DAP	1.1938	0.499
41DAP/39DAP	1.9328	0.407
42DAP/41DAP	0.90525	0.538
43DAP/42DAP	0.86306	0.089
47DAP/43DAP	1.0797	0.674
52DAP/47DAP	1.01036	0.986
57DAP/52DAP	1.04041	0.838
57DAP/7DAP	0.84973	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84366	0.086
17DAP/reference	0.99273	0.693
27DAP/reference	1.13607	0.453
39DAP/reference	0.95843	0.411
41DAP/reference	1.00333	0.811
42DAP/reference	0.96571	0.338
43DAP/reference	1.00256	0.694
47DAP/reference	0.87232	0.293
52DAP/reference	1.07298	0.401
57DAP/reference	0.98721	0.569

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06463	0.863
17DAP/reference	1.21992	0.243
27DAP/reference	0.74496	0.188
39DAP/reference	0.73137	0.067
41DAP/reference	0.76937	0.021
42DAP/reference	1.06606	1
43DAP/reference	1.3598	0.116
47DAP/reference	1.00736	0.73
52DAP/reference	1.22763	0.036
57DAP/reference	1.41337	0.523

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15243	0.397
17DAP/reference	0.96909	0.601
27DAP/reference	1.2026	0.085
39DAP/reference	1.16149	0.218
41DAP/reference	0.92832	0.293
42DAP/reference	1.02025	1
43DAP/reference	0.87618	0.197
47DAP/reference	1.05644	1
52DAP/reference	1.03509	1
57DAP/reference	0.92747	0.444

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10831	0.966
26DAP/20DAP	1.0906	0.753
34DAP/26DAP	0.99207	0.944
51DAP/34DAP	1.35475	0.692
52DAP/51DAP	1.63511	0.054
53DAP/52DAP	0.81567	0.612
55DAP/53DAP	1.14421	N/A
57DAP/55DAP	0.94494	0.799
62DAP/57DAP	1.26488	0.35
68DAP/62DAP	1.05707	1
68DAP/14DAP	1.7761	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.70254	0.03

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.89694	0.487
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.40723	N/A
Mature Eggplant/Ripe Tomato	1.04266	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.27357	0.877
1-1-2/M82	1.08746	1
12-2/M82	1.18485	N/A
12-4/M82	1.156	1
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	1.49135	0.695
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	0.89721	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.31336	1
5-3/M82	0.72143	0.642
6-2/M82	N/A	N/A
6-3/M82	0.75825	N/A
7-1/M82	N/A	N/A
7-2/M82	1.29997	0.385
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.09193	N/A
IL2-6/WTpooled	0.80115	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.57533	N/A
IL12-4/WTpooled	0.81168	1
IL1-4/WTpooled	1.24305	N/A
WT/WTpooled	0.99996	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	1.07871	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.18563	0.758
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.01648	1
DC3000/delta hrp 24h	2.41528	0.025

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.16255	0.053
DC3000 delta B/DC3000 delta AB	1.00704	1

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	0.86738	1
Var 0h	0.95566	1
Var 12h I row2-row1	1.21836	0.379
Var 12h NI row2-row1	0.88547	0.713
Var 36h I row2-row1	0.8514	0.805
Var 36h NI row2-row1	0.94874	0.706
Var 60h I row2-row1	0.74596	0.293
Var 60h NI row2-row1	1.09684	0.904
Time course 0hI-0hNI	1.04735	0.833
Time course 12hI-12hNI	0.96053	0.646
Time course 36hI-36hNI	0.98318	0.611
Time course 60hI-60hNI	1.16136	0.137

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	0.85741	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.15229	0.194

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.30818	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	0.93899	1
Manapal/WT (red)	0.65473	0.188