Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.9.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16281	0.964
27DAP/17DAP	0.9332	0.877
39DAP/27DAP	5.06949	0.031
41DAP/39DAP	1.08679	0.722
42DAP/41DAP	0.85332	0.774
43DAP/42DAP	1.77705	0.861
47DAP/43DAP	0.55666	0.051
52DAP/47DAP	0.83046	0.562
57DAP/52DAP	0.8412	0.768

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.41026	0.121
17DAP/reference	0.83042	0.024
27DAP/reference	0.73457	0.012
39DAP/reference	1.11359	0.828
41DAP/reference	0.86701	0.201
42DAP/reference	1.82277	0.001
43DAP/reference	2.09543	0.006
47DAP/reference	1.31006	0.078
52DAP/reference	0.74024	0.018
57DAP/reference	0.92911	0.358

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.3919	0.027
27DAP/17DAP	1.48296	0.038
39DAP/27DAP	2.48015	0.047
41DAP/39DAP	1.77391	0.455
42DAP/41DAP	0.94229	0.625
43DAP/42DAP	1.34117	0.079
47DAP/43DAP	1.28748	0.119
52DAP/47DAP	0.59883	0.064
57DAP/52DAP	1.05688	0.926
57DAP/7DAP	1.61642	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28636	0.091
17DAP/reference	0.98945	0.599
27DAP/reference	1.41264	0.01
39DAP/reference	1.06646	0.282
41DAP/reference	1.12567	0.28
42DAP/reference	1.43708	0.011
43DAP/reference	1.63875	0.009
47DAP/reference	2.58985	0.014
52DAP/reference	1.56117	0.007
57DAP/reference	0.90703	0.183

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21036	0.146
17DAP/reference	0.75222	0.012
27DAP/reference	1.34072	0.033
39DAP/reference	1.06697	0.824
41DAP/reference	0.90313	0.148
42DAP/reference	1.11728	0.317
43DAP/reference	1.50863	0.161
47DAP/reference	1.66099	0.041
52DAP/reference	0.64457	0.004
57DAP/reference	1.3006	0.221

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.35994	0.039
17DAP/reference	0.84487	0.189
27DAP/reference	1.02332	0.871
39DAP/reference	1.45439	0.004
41DAP/reference	1.1964	0.022
42DAP/reference	2.07151	0.007
43DAP/reference	2.221	0.007
47DAP/reference	1.31639	0.042
52DAP/reference	1.36669	0.115
57DAP/reference	0.6048	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99303	1
26DAP/20DAP	1.20287	0.818
34DAP/26DAP	1.78446	0.819
51DAP/34DAP	0.9194	0.631
52DAP/51DAP	2.3442	0.045
53DAP/52DAP	1.13882
55DAP/53DAP	1.25611	0.387
57DAP/55DAP	0.776	0.213
62DAP/57DAP	1.29568	0.115
68DAP/62DAP	1.40264	0.914
68DAP/14DAP	0.77642	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	11.2045	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.59895	0.213
Mature Green Tomato/Ripe Tomato	0.48827	0.019
Immature Eggplant/Mature Eggplant	15.9889	0.05
Ripe Pepper/Ripe Tomato	0.10696	0.224
Mature Eggplant/Ripe Tomato	0.24672	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.45035
1-1-2/M82	1.85678	1
12-2/M82	N/A	N/A
12-4/M82	1.53477	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	2.02131
3-2/M82	1.20896	0.84
4-1-1/M82	1.59195	1
4-1/M82	3.14462	0.466
4-3-2/M82	2.07893	0.508
4-3/M82	3.94862	0.268
5-3/M82	0.90318	1
6-2/M82	4.46527	1
6-3/M82	0.3657
7-1/M82	0.85393	0.443
7-2/M82	1.08665
9-3-2/M82	2.74685	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.24522	1
IL2-6/WTpooled	1.24377	0.419
IL7-5/WTpooled	0.2505	1
IL7-3/WTpooled	1.25111	1
IL12-4/WTpooled	0.54932	0.543
IL1-4/WTpooled	0.78861	0.402
WT/WTpooled	0.8973	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	1.31695	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07566	0.921
DC3000/delta hrp 6h	1.15771	1
DC3000/delta hrp 12h	1.11197	1
DC3000/delta hrp 24h	6.02708	0.017

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.75908	0.042
DC3000 delta B/DC3000 delta AB	2.83047	0.023

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.49376	0.227
Exp 36h	2.54326	0.349
Exp 60h	2.74414	0.22

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01448	1
Var 0h	0.91382	0.933
Var 12h I row2-row1	1.1943	0.296
Var 12h NI row2-row1	1.12356	0.649
Var 36h I row2-row1	1.01586	1
Var 36h NI row2-row1	1.05051	0.852
Var 60h I row2-row1	1.07284	1
Var 60h NI row2-row1	0.74032	0.431
Time course 0hI-0hNI	1.02425	0.867
Time course 12hI-12hNI	1.77913	0.005
Time course 36hI-36hNI	4.30127	0.004
Time course 60hI-60hNI	5.83022	0.008

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)	0.67343	0.246
transgenic ySAMdc/azygous control (breaker)	1.12327	0.248
transgenic ySAMdc/azygous control (red)	1.30636	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01784	0.495

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.60587	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.66368	1
Manapal/WT (break)	0.96417	1
Manapal/WT (red)	1.29581	0.413