Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.4.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.79325	0.232
27DAP/17DAP	1.44076	0.681
39DAP/27DAP	1.48143	0.092
41DAP/39DAP	0.81835	0.302
42DAP/41DAP	1.03368	1
43DAP/42DAP	1.03307	0.937
47DAP/43DAP	1.3014	0.633
52DAP/47DAP	1.1003	0.879
57DAP/52DAP	1.23713	0.902

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94859	0.371
17DAP/reference	0.84137	0.085
27DAP/reference	1.16122	0.539
39DAP/reference	0.99803	1
41DAP/reference	0.71453	0.085
42DAP/reference	1.09405	0.2
43DAP/reference	1.17316	0.812
47DAP/reference	1.0894	0.575
52DAP/reference	1.32888	0.088
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.35625	0.129
27DAP/17DAP	0.8259	0.446
39DAP/27DAP	0.97641	0.87
41DAP/39DAP	1.02101	1
42DAP/41DAP	0.83337	0.034
43DAP/42DAP	1.08509	0.351
47DAP/43DAP	0.98516	0.928
52DAP/47DAP	1.07701	0.73
57DAP/52DAP	1.06704	0.911
57DAP/7DAP	0.94488	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.9363	0.024
17DAP/reference	1.38291	0.007
27DAP/reference	1.24813	0.023
39DAP/reference	1.91511	0.006
41DAP/reference	1.86456	0.041
42DAP/reference	1.41584	0.03
43DAP/reference	1.60748	0.009
47DAP/reference	2.28599	0.022
52DAP/reference	1.56718	0.013
57DAP/reference	2.03335	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00879	0.77
17DAP/reference	1.01568	1
27DAP/reference	1.20177	0.446
39DAP/reference	1.19311	0.477
41DAP/reference	1.0701	0.573
42DAP/reference	1.23672	0.053
43DAP/reference	0.87809	0.243
47DAP/reference	1.42066	0.008
52DAP/reference	1.0604	1
57DAP/reference	0.86764	0.156

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.59196	0.027
17DAP/reference	0.96058	0.601
27DAP/reference	1.14712	0.156
39DAP/reference	1.20832	0.146
41DAP/reference	1.52565	0.276
42DAP/reference	1.18921	0.138
43DAP/reference	1.2583	0.042
47DAP/reference	1.13901	0.585
52DAP/reference	1.85209	0.035
57DAP/reference	1.43743	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95955	1
26DAP/20DAP	1.46249	0.103
34DAP/26DAP	0.84678	0.267
51DAP/34DAP	1.01241	0.962
52DAP/51DAP	0.92801	1
53DAP/52DAP	1.1001	0.768
55DAP/53DAP	0.88835	0.303
57DAP/55DAP	1.19569	0.643
62DAP/57DAP	0.87297	0.681
68DAP/62DAP	1.27692	0.646
68DAP/14DAP	1.18907	0.958

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.13869	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.99534	0.805
Mature Green Tomato/Ripe Tomato	1.23293	0.299
Immature Eggplant/Mature Eggplant	0.65723	0.064
Ripe Pepper/Ripe Tomato	0.71658	0.224
Mature Eggplant/Ripe Tomato	0.84064	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.70373	0.605
1-1-2/M82	1.07152	1
12-2/M82	0.99681	1
12-4/M82	0.87968	1
1-3/M82	1.57917	1
2-1-1/M82	0.84318	0.683
2-1/M82	0.91286	0.74
2-6/M82	0.74089	0.501
3-2/M82	0.74633	1
4-1-1/M82	0.84176	1
4-1/M82	0.56385
4-3-2/M82	0.95909
4-3/M82	1.09472	1
5-3/M82	1.12032	0.427
6-2/M82	0.66111	0.481
6-3/M82	1.16796
7-1/M82	1.13673
7-2/M82	0.86704	0.796
9-3-2/M82	0.77519	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.93377	1
IL2-6/WTpooled	1.10251	0.584
IL7-5/WTpooled	1.18595	0.792
IL7-3/WTpooled	0.89452	1
IL12-4/WTpooled	1.07549	0.695
IL1-4/WTpooled	1.35564	1
WT/WTpooled	0.99932	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	1.0038	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00656	1
DC3000/delta hrp 6h	0.93147	0.95
DC3000/delta hrp 12h	1.01139	1
DC3000/delta hrp 24h	0.89435	0.225

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.8431	0.436
DC3000 delta B/DC3000 delta AB	1.01106	0.703

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.39732	1
Exp 36h	0.99059	1
Exp 60h	1.25069	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	0.86727
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.90311	0.309
transgenic ySAMdc/azygous control (breaker)	1.1599	0.248
transgenic ySAMdc/azygous control (red)	0.95804	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.56668	0.04

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.66672	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.7705	0.172
Manapal/WT (break)	0.75343	0.299
Manapal/WT (red)	0.90053	0.36