Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.14.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9791	0.823
27DAP/17DAP	0.94621	0.923
39DAP/27DAP	1.23936	0.548
41DAP/39DAP	0.81031	0.315
42DAP/41DAP	1.02771	1
43DAP/42DAP	1.04158	1
47DAP/43DAP	1.02183	0.902
52DAP/47DAP	1.51797	0.307
57DAP/52DAP	1.04281	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03239	0.735
17DAP/reference	0.9948	0.904
27DAP/reference	1.02832	0.831
39DAP/reference	1.13253	0.079
41DAP/reference	1.05518	0.365
42DAP/reference	1.16236	0.016
43DAP/reference	1.0812	0.233
47DAP/reference	1.12164	0.052
52DAP/reference	1.1205	0.134
57DAP/reference	1.23242	0.04

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20991	0.096
27DAP/17DAP	0.85364	0.475
39DAP/27DAP	1.10701	0.575
41DAP/39DAP	0.99448	1
42DAP/41DAP	1.00871	1
43DAP/42DAP	1.13403	0.103
47DAP/43DAP	0.96532	0.774
52DAP/47DAP	1.13909	0.508
57DAP/52DAP	1.02243	0.984
57DAP/7DAP	1.48722	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9188	0.361
17DAP/reference	0.92323	0.124
27DAP/reference	1.2907	0.014
39DAP/reference	1.01306	1
41DAP/reference	0.88548	0.062
42DAP/reference	1.11893	0.1
43DAP/reference	1.00763	1
47DAP/reference	1.0801	0.235
52DAP/reference	1.19377	0.007
57DAP/reference	1.15105	0.023

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16889	0.289
17DAP/reference	1.19711	0.043
27DAP/reference	1.54743	0.019
39DAP/reference	1.31225	0.016
41DAP/reference	1.27094	0.015
42DAP/reference	1.4884	0.009
43DAP/reference	1.56983	0.011
47DAP/reference	1.62106	0.008
52DAP/reference	1.30396	0.013
57DAP/reference	1.41849	0.01

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78873	0.038
17DAP/reference	1.08278	0.738
27DAP/reference	0.8945	0.092
39DAP/reference	0.97019	0.43
41DAP/reference	1.17964	0.286
42DAP/reference	1.14279	0.313
43DAP/reference	1.09022	0.572
47DAP/reference	1.27878	0.01
52DAP/reference	1.07585	0.683
57DAP/reference	1.3288	0.015

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.92358	1
26DAP/20DAP	1.02349	1
34DAP/26DAP	1.41618	0.819
51DAP/34DAP	0.83393	0.161
52DAP/51DAP	1.01339	0.954
53DAP/52DAP	1.10303	0.819
55DAP/53DAP	1.12269	0.555
57DAP/55DAP	0.90229	0.539
62DAP/57DAP	0.9373	0.681
68DAP/62DAP	0.80139	0.245
68DAP/14DAP	1.04065	0.958

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.57276	0.041

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.57414	0.059
Mature Green Tomato/Ripe Tomato	0.95991	0.611
Immature Eggplant/Mature Eggplant	1.05786	0.3
Ripe Pepper/Ripe Tomato	0.45868	0.224
Mature Eggplant/Ripe Tomato	0.77107	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02923	1
1-1-2/M82	0.9593	1
12-2/M82	1.56377	1
12-4/M82	0.97252	1
1-3/M82	0.96697	1
2-1-1/M82	0.92882	1
2-1/M82	0.86823	0.74
2-6/M82	1.03388	1
3-2/M82	0.87642	0.455
4-1-1/M82	0.88873	1
4-1/M82	1.35498	1
4-3-2/M82	1.07623	0.241
4-3/M82	1.12815	0.268
5-3/M82	0.99951	1
6-2/M82	0.74611
6-3/M82	N/A	N/A
7-1/M82	0.81666	1
7-2/M82	0.96722	1
9-3-2/M82	1.36571	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.55636
IL2-6/WTpooled	0.80042	0.473
IL7-5/WTpooled	0.82084
IL7-3/WTpooled	1.09852	1
IL12-4/WTpooled	0.99955	1
IL1-4/WTpooled	0.83112
WT/WTpooled	1.00086	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	1.00727	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09515	0.758
DC3000/delta hrp 6h	1.05061	1
DC3000/delta hrp 12h	0.91343	1
DC3000/delta hrp 24h	1.02995	0.743

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.56072
DC3000 delta B/DC3000 delta AB	0.87489	0.445

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04514	0.254
Exp 36h	0.89638	0.504
Exp 60h	1.15392	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0087	1
Var 0h	0.98318	1
Var 12h I row2-row1	0.99833	1
Var 12h NI row2-row1	0.93751	0.713
Var 36h I row2-row1	0.81137	0.805
Var 36h NI row2-row1	0.95122	0.743
Var 60h I row2-row1	0.99548	1
Var 60h NI row2-row1	0.9135	0.756
Time course 0hI-0hNI	1.0111	0.867
Time course 12hI-12hNI	1.07119	0.415
Time course 36hI-36hNI	1.07836	0.128
Time course 60hI-60hNI	1.26805	0.012

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)	0.84082	0.235
transgenic ySAMdc/azygous control (breaker)	0.73585	0.137
transgenic ySAMdc/azygous control (red)	0.90001	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07744	0.05

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.83447	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.99659	1
Manapal/WT (break)	0.82432	0.333
Manapal/WT (red)	1.25378	0.413