Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.5.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9748	0.788
27DAP/17DAP	0.93786	0.839
39DAP/27DAP	1.68652	0.113
41DAP/39DAP	0.72361	0.132
42DAP/41DAP	0.84992	1
43DAP/42DAP	1.23628	1
47DAP/43DAP	0.82235	0.433
52DAP/47DAP	0.88555	0.675
57DAP/52DAP	1.29159	0.883

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.70304	0.014
17DAP/reference	1.33326	0.057
27DAP/reference	1.30312	0.184
39DAP/reference	1.34793	0.181
41DAP/reference	1.51751	0.058
42DAP/reference	1.80608	0.001
43DAP/reference	1.34713	0.012
47DAP/reference	1.60428	0.001
52DAP/reference	1.18763	0.01
57DAP/reference	1.26524	0.017

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14373	0.728
27DAP/17DAP	1.42899	0.075
39DAP/27DAP	0.72411	0.204
41DAP/39DAP	1.46086	1
42DAP/41DAP	1.11399	1
43DAP/42DAP	0.89946	0.538
47DAP/43DAP	0.88153	0.402
52DAP/47DAP	1.39857	0.283
57DAP/52DAP	1.43679	0.179
57DAP/7DAP	1.11533	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.30268	0.024
17DAP/reference	1.94636	0.009
27DAP/reference	2.08682	0.007
39DAP/reference	1.92596	0.005
41DAP/reference	2.02991	0.01
42DAP/reference	2.12691	0.008
43DAP/reference	2.00444	0.006
47DAP/reference	2.06672	0.014
52DAP/reference	2.04351	0.007
57DAP/reference	1.93723	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.36978	0.187
17DAP/reference	1.47359	0.049
27DAP/reference	2.06909	0.015
39DAP/reference	1.63428	0.011
41DAP/reference	1.60319	0.005
42DAP/reference	2.13107	0.007
43DAP/reference	0.97513	0.516
47DAP/reference	1.77862	0.008
52DAP/reference	1.33249	0.015
57DAP/reference	0.89488	0.243

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.30069	0.015
17DAP/reference	1.1221	0.531
27DAP/reference	1.7365	0.016
39DAP/reference	1.83451	0.007
41DAP/reference	1.3024	0.008
42DAP/reference	2.09919	0.009
43DAP/reference	2.3076	0.007
47DAP/reference	1.11508	0.792
52DAP/reference	2.22527	0.03
57DAP/reference	1.75456	0.018

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10878	0.966
26DAP/20DAP	2.99566	0.342
34DAP/26DAP	2.01512	1
51DAP/34DAP	1.92201	0.416
52DAP/51DAP	1.98308	0.037
53DAP/52DAP	0.80625	0.21
55DAP/53DAP	0.91073	0.5
57DAP/55DAP	0.89055	0.433
62DAP/57DAP	1.63121	0.007
68DAP/62DAP	0.79351	0.314
68DAP/14DAP	1.67798	0.027

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.20298	0.782

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.5004	0.093
Mature Green Tomato/Ripe Tomato	1.37901
Immature Eggplant/Mature Eggplant	1.59502	0.05
Ripe Pepper/Ripe Tomato	0.93438	1
Mature Eggplant/Ripe Tomato	0.96808	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.27706	1
12-2/M82	N/A	N/A
12-4/M82	1.20956	1
1-3/M82	2.78908
2-1-1/M82	0.81208
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	1.44792	0.717
4-1-1/M82	0.65756
4-1/M82	3.34113
4-3-2/M82	1.28198	0.262
4-3/M82	1.47146	1
5-3/M82	1.06074	1
6-2/M82	N/A	N/A
6-3/M82	1.02949
7-1/M82	1.14089
7-2/M82	1.17161
9-3-2/M82	1.36608	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.08269	1
IL2-6/WTpooled	1.06894	1
IL7-5/WTpooled	0.93595	1
IL7-3/WTpooled	0.73144	0.418
IL12-4/WTpooled	1.01073	1
IL1-4/WTpooled	1.16378	1
WT/WTpooled	0.90788	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	1.41669	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01612	1
DC3000/delta hrp 6h	1.05918
DC3000/delta hrp 12h	1.25426	1
DC3000/delta hrp 24h	1.27514	0.103

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.97419
DC3000 delta B/DC3000 delta AB	1.30001	0.199

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02401	1
Exp 36h	2.06695	0.489
Exp 60h	2.0554	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01119	1
Var 0h	1.0275	1
Var 12h I row2-row1	1.18132	0.654
Var 12h NI row2-row1	0.99896	1
Var 36h I row2-row1	0.94096	1
Var 36h NI row2-row1	1.23133	1
Var 60h I row2-row1	0.72952	0.292
Var 60h NI row2-row1	0.86984	0.932
Time course 0hI-0hNI	0.96727	0.801
Time course 12hI-12hNI	1.07125	0.56
Time course 36hI-36hNI	1.24526	0.015
Time course 60hI-60hNI	1.81865	0.029

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)	1.11933	0.571
transgenic ySAMdc/azygous control (breaker)	0.72633	0.173
transgenic ySAMdc/azygous control (red)	1.03828	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.25596	0.213

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.63542	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.01066	1
Manapal/WT (break)	1.19824	0.381
Manapal/WT (red)	1.36831	0.134