Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.1.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.38897	0.037
27DAP/17DAP	0.56343	0.039
39DAP/27DAP	1.26578	0.527
41DAP/39DAP	0.81716	0.33
42DAP/41DAP	0.74513	0.774
43DAP/42DAP	0.77938	0.709
47DAP/43DAP	1.03916	0.84
52DAP/47DAP	0.94671	0.832
57DAP/52DAP	1.16121	0.987

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9047	0.154
17DAP/reference	0.8065	0.028
27DAP/reference	0.80904	0.039
39DAP/reference	0.76994	0.019
41DAP/reference	0.76348	0.039
42DAP/reference	0.86392	0.129
43DAP/reference	0.84651	0.113
47DAP/reference	0.91707	0.174
52DAP/reference	1.12227	1
57DAP/reference	1.01334	0.767

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.28745	0.1
27DAP/17DAP	0.72145	0.144
39DAP/27DAP	0.82586	0.265
41DAP/39DAP	0.96646	0.973
42DAP/41DAP	0.85081	0.515
43DAP/42DAP	1.00613	1
47DAP/43DAP	0.96366	0.896
52DAP/47DAP	1.36817	0.945
57DAP/52DAP	1.26844	0.442
57DAP/7DAP	1.46214	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00354	1
17DAP/reference	0.93266	0.167
27DAP/reference	0.87576	0.135
39DAP/reference	0.84527	0.043
41DAP/reference	1.27101	0.223
42DAP/reference	1.09094	0.686
43DAP/reference	0.69066	0.022
47DAP/reference	0.73006	0.079
52DAP/reference	0.60428	0.017
57DAP/reference	0.5971	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76851	0.043
17DAP/reference	0.89005	0.008
27DAP/reference	0.78061	0.048
39DAP/reference	0.70857	0.011
41DAP/reference	0.75972	0.011
42DAP/reference	0.74379	0.012
43DAP/reference	0.71979	0.018
47DAP/reference	0.60518	0.011
52DAP/reference	0.80074	0.004
57DAP/reference	0.77966	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91735	0.197
17DAP/reference	0.94389	0.508
27DAP/reference	0.79402	0.045
39DAP/reference	0.94391	0.246
41DAP/reference	0.70075	0.018
42DAP/reference	0.6234	0.028
43DAP/reference	0.72022	0.023
47DAP/reference	0.69836	0.008
52DAP/reference	0.60266	0.051
57DAP/reference	0.68326	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08712	0.817
26DAP/20DAP	0.88805	1
34DAP/26DAP	0.94563	0.927
51DAP/34DAP	0.57788	0.193
52DAP/51DAP	0.95125	1
53DAP/52DAP	1.24984	0.398
55DAP/53DAP	1.97595	0.048
57DAP/55DAP	0.99207	0.925
62DAP/57DAP	0.86253
68DAP/62DAP	1.11261	0.831
68DAP/14DAP	1.55077

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.70906	0.031

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.26222	0.089
Mature Green Tomato/Ripe Tomato	5.94263	0.015
Immature Eggplant/Mature Eggplant	2.93668	0.05
Ripe Pepper/Ripe Tomato	0.70269
Mature Eggplant/Ripe Tomato	13.2535	0.373

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	N/A	N/A
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	1.0654	1
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	0.98449	1
IL2-6/WTpooled	1.0085	1
IL7-5/WTpooled	0.92121	1
IL7-3/WTpooled	1.0545	1
IL12-4/WTpooled	1.25519	0.483
IL1-4/WTpooled	1.03038	1
WT/WTpooled	1.00748	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	1.1826	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03191	0.921
DC3000/delta hrp 6h	0.96473	0.95
DC3000/delta hrp 12h	0.95139	1
DC3000/delta hrp 24h	2.4999	0.041

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.74456	0.025
DC3000 delta B/DC3000 delta AB	0.71148	0.026

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04368	1
Exp 36h	0.77944	0.456
Exp 60h	0.75934	0.386

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	0.86147	0.457
Var 12h I row2-row1	0.71941	0.357
Var 12h NI row2-row1	1.08421	1
Var 36h I row2-row1	0.71057	0.203
Var 36h NI row2-row1	1.14974	1
Var 60h I row2-row1	0.88847	0.582
Var 60h NI row2-row1	1.04902	1
Time course 0hI-0hNI	1.17581	0.63
Time course 12hI-12hNI	0.93085	0.497
Time course 36hI-36hNI	0.75304	0.023
Time course 60hI-60hNI	0.41681	0.006

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)	0.92643	0.229
transgenic ySAMdc/azygous control (breaker)	1.35308	0.162
transgenic ySAMdc/azygous control (red)	1.1283	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.90858	0.143

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.90056	0.223

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.25428	0.086
Manapal/WT (break)	1.23137	0.381
Manapal/WT (red)	0.90835	0.728