Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.5.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.58187	0.211
27DAP/17DAP	0.79738	0.819
39DAP/27DAP	2.17255	0.635
41DAP/39DAP	1.15452	0.929
42DAP/41DAP	1.2169	0.722
43DAP/42DAP	1.40517	0.327
47DAP/43DAP	2.07358	0.349
52DAP/47DAP	0.8847	0.559
57DAP/52DAP	1.6089	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74633	0.074
17DAP/reference	0.86466	0.097
27DAP/reference	0.81942	0.157
39DAP/reference	1.07704	0.603
41DAP/reference	0.7629	0.049
42DAP/reference	0.95893	0.25
43DAP/reference	1.36945	0.01
47DAP/reference	1.66429	0.001
52DAP/reference	1.75063	0.014
57DAP/reference	1.3384	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98053	0.75
27DAP/17DAP	1.61072	0.639
39DAP/27DAP	0.90482	0.721
41DAP/39DAP	0.77267	0.547
42DAP/41DAP	0.82006	0.362
43DAP/42DAP	1.0096	0.991
47DAP/43DAP	1.22714	0.827
52DAP/47DAP	1.43969	0.334
57DAP/52DAP	0.99072	0.852
57DAP/7DAP	1.28732	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88172	0.086
17DAP/reference	0.92849	0.192
27DAP/reference	0.93414	0.071
39DAP/reference	0.7938	0.015
41DAP/reference	0.7405	0.037
42DAP/reference	0.70713	0.011
43DAP/reference	0.67511	0.011
47DAP/reference	1.17954	0.67
52DAP/reference	0.66731	0.017
57DAP/reference	0.84773	0.077

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79727	0.058
17DAP/reference	1.01595	0.594
27DAP/reference	0.91332	0.327
39DAP/reference	0.93546	0.404
41DAP/reference	0.82521	0.133
42DAP/reference	0.95688	0.433
43DAP/reference	1.01832	0.863
47DAP/reference	0.83305	0.11
52DAP/reference	0.91414	0.259
57DAP/reference	0.81273	0.099

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80877	0.077
17DAP/reference	0.89246	0.239
27DAP/reference	0.75586	0.041
39DAP/reference	0.74235	0.023
41DAP/reference	0.91195	0.064
42DAP/reference	0.92267	0.445
43DAP/reference	0.97606	0.484
47DAP/reference	1.85265	0.005
52DAP/reference	1.4529	0.749
57DAP/reference	1.74103	0.079

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02509	1
26DAP/20DAP	0.69686
34DAP/26DAP	1.31536	1
51DAP/34DAP	0.60606	0.071
52DAP/51DAP	1.16519	0.534
53DAP/52DAP	0.80933	0.663
55DAP/53DAP	1.09201	0.951
57DAP/55DAP	1.32278	0.841
62DAP/57DAP	0.58239	0.004
68DAP/62DAP	1.00379	1
68DAP/14DAP	2.36116	0.063

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.05118

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.28806	0.081
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.33693	0.224
Mature Eggplant/Ripe Tomato	0.01296

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	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	0.95825
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	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.13959	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.66424	0.587
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.71157	0.554
IL1-4/WTpooled	1.05178
WT/WTpooled	0.48876	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	0.91436	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91358	1
DC3000/delta hrp 6h	1.11017	1
DC3000/delta hrp 12h	0.84234	1
DC3000/delta hrp 24h	0.41156	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.82078	1
Exp 36h	0.73936	0.589
Exp 60h	0.601	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02703	1
Var 0h	1.1154	0.936
Var 12h I row2-row1	1.71058	0.283
Var 12h NI row2-row1	0.91856	0.627
Var 36h I row2-row1	1.09563	0.368
Var 36h NI row2-row1	1.21738
Var 60h I row2-row1	0.95236	0.582
Var 60h NI row2-row1	1.04417	0.904
Time course 0hI-0hNI	0.93529	0.631
Time course 12hI-12hNI	0.77471	0.519
Time course 36hI-36hNI	1.05948	0.513
Time course 60hI-60hNI	1.37547	0.069

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)	0.99972	1
transgenic ySAMdc/azygous control (breaker)	0.77211	0.251
transgenic ySAMdc/azygous control (red)	1.0465	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.86924	0.06

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.57866	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.53224	0.105
Manapal/WT (break)	1.323	1
Manapal/WT (red)	0.99624	0.863