Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.19.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17797	0.755
27DAP/17DAP	1.11933	0.859
39DAP/27DAP	1.32716	0.677
41DAP/39DAP	1.06034	1
42DAP/41DAP	1.05127	0.997
43DAP/42DAP	0.8985	0.865
47DAP/43DAP	1.51665	0.377
52DAP/47DAP	0.85672	0.615
57DAP/52DAP	1.08509	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.55581	0.011
17DAP/reference	1.55635	0.02
27DAP/reference	1.47182	0.066
39DAP/reference	1.31176	0.136
41DAP/reference	1.91381	0.012
42DAP/reference	1.42768	0.001
43DAP/reference	1.16997	0.089
47DAP/reference	1.27067	0.34
52DAP/reference	1.47541	0.009
57DAP/reference	1.33065	0.122

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0293	0.91
27DAP/17DAP	1.04873	0.9
39DAP/27DAP	1.08296	0.403
41DAP/39DAP	1.13201	0.439
42DAP/41DAP	0.94158	0.62
43DAP/42DAP	0.99865	1
47DAP/43DAP	1.03739	0.914
52DAP/47DAP	1.14209	0.549
57DAP/52DAP	1.12222	0.431
57DAP/7DAP	1.0354	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84318	0.115
17DAP/reference	0.76417	0.012
27DAP/reference	0.75981	0.01
39DAP/reference	0.88106	0.095
41DAP/reference	0.82405	0.028
42DAP/reference	0.8958	0.151
43DAP/reference	0.72014	0.016
47DAP/reference	0.79787	0.222
52DAP/reference	0.81021	0.053
57DAP/reference	0.96548	0.426

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30921	0.304
17DAP/reference	1.555	0.012
27DAP/reference	1.48754	0.026
39DAP/reference	1.34884	0.141
41DAP/reference	1.37463	0.099
42DAP/reference	1.55251	0.009
43DAP/reference	1.5858	0.047
47DAP/reference	1.43577	0.013
52DAP/reference	1.33781	0.038
57DAP/reference	1.04156	0.771

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85372	0.158
17DAP/reference	0.83738	0.249
27DAP/reference	0.7931	0.031
39DAP/reference	0.96441	0.504
41DAP/reference	0.91152	0.293
42DAP/reference	0.9987	0.816
43DAP/reference	1.0507	1
47DAP/reference	1.02154	0.667
52DAP/reference	0.92883	0.493
57DAP/reference	1.07791	0.717

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04869	1
26DAP/20DAP	0.9077	0.512
34DAP/26DAP	1.43648	0.19
51DAP/34DAP	0.91966	0.571
52DAP/51DAP	1.21837	0.167
53DAP/52DAP	0.93066	0.604
55DAP/53DAP	1.17785	0.244
57DAP/55DAP	0.86073	0.415
62DAP/57DAP	1.12052	0.569
68DAP/62DAP	0.80541	0.641
68DAP/14DAP	0.63429	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.73167	0.03

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.53339	0.113
Mature Green Tomato/Ripe Tomato	0.68237	0.066
Immature Eggplant/Mature Eggplant	0.85271
Ripe Pepper/Ripe Tomato	0.53868	0.293
Mature Eggplant/Ripe Tomato	0.26295	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.14141
1-1-2/M82	1.1258	1
12-2/M82	0.9198	0.955
12-4/M82	1.09052	1
1-3/M82	1.59973	0.26
2-1-1/M82	1.18723	1
2-1/M82	N/A	N/A
2-6/M82	0.72352	1
3-2/M82	0.80952
4-1-1/M82	1.01101
4-1/M82	0.63634
4-3-2/M82	0.77208	1
4-3/M82	1.237	1
5-3/M82	1.05488	1
6-2/M82	0.62981	0.497
6-3/M82	0.90936	1
7-1/M82	1.3046	0.539
7-2/M82	1.04806	1
9-3-2/M82	1.55463

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.24802
IL12-4/WTpooled	1.15844	0.52
IL1-4/WTpooled	1.56569
WT/WTpooled	0.96944	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	0.99336	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.17473	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.47942	1
DC3000/delta hrp 24h	1.07838	0.743

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.04743	0.049
DC3000 delta B/DC3000 delta AB	1.17861	0.298

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03862	1
Exp 36h	1.25956	1
Exp 60h	0.95342	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01391	1
Var 0h	0.71184	0.933
Var 12h I row2-row1	0.89762	0.467
Var 12h NI row2-row1	0.89489	0.713
Var 36h I row2-row1	1.03545	1
Var 36h NI row2-row1	0.95175	0.584
Var 60h I row2-row1	1.04093	0.523
Var 60h NI row2-row1	0.97355	1
Time course 0hI-0hNI	0.93526	0.54
Time course 12hI-12hNI	1.1175	0.186
Time course 36hI-36hNI	1.15136	0.355
Time course 60hI-60hNI	1.03655	0.495

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)	0.867	0.377
transgenic ySAMdc/azygous control (breaker)	1.00972	1
transgenic ySAMdc/azygous control (red)	0.98375	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.89434	0.069

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95545	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.03018	1
Manapal/WT (red)	1.29364	0.133