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| Status |
Public on May 25, 2015 |
| Title |
Identification of Replication Timing Domains Using DNN-HMM |
| Sample organism |
Homo sapiens |
| Experiment type |
Third-party reanalysis
Other
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| Summary |
Purpose: Sixteen GSM Samples from GSE34399 was used to identify four different types of replication timing domains.
Methods: 1. Chromosome 1 of Bj_Rep1 was manually annotated. 2. We developed a new supervised method called DNN-HMM (Deep Neural Network-Hidden Markov Model), and used the manual annotation as the training set to learn a model. 3. The model learnt in Step 2 was used to divide the un-annotated Repli-seq datas into four different replication domains (early replication domain, down transition zone, late replication domain, up transition zone).
Result: We used DNN-HMM to identify four different replication timing domains respectively in fifteen cell lines. The accuracy of identification was about 87%, and the overlapping percentage of two independent replicates of Bj cell line was about 83%.
Data File Formats :(bed)
chrom - The name of the chromosome
chromStart - The starting position of the feature in the chromosome
chromEnd - The ending position of the feature in the chromosome
category - The domain identified (denoted by: ERD, short for early replication domain; DTZ, short for down transition zone; LRD, short for late replication domain; UTZ, short for up transition zone)
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| Overall design |
Repli-seq datas from GSE34399 were used as the raw datas. After mapping and normalization, the signals from six cell cycle fractions: G1/G1b, S1, S2, S3, S4, G2 (six fraction profile) were merged into a matrix. The six-dimensional matrix then was used as input of DNN-HMM to identify replication timing domains.
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| Contributor(s) |
Shu W, Liu F |
| Citation(s) |
26545821 |
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| Submission date |
Jan 10, 2014 |
| Last update date |
Nov 23, 2015 |
| Contact name |
Wenjie Shu |
| E-mail(s) |
shuwj@bmi.ac.cn
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| Organization name |
Beijing Institute of Radiation Medicine
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| Street address |
Taiping Road 27
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| City |
Beijing |
| ZIP/Postal code |
100850 |
| Country |
China |
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| Relations |
| Reanalysis of |
GSM923439 |
| Reanalysis of |
GSM923440 |
| Reanalysis of |
GSM923441 |
| Reanalysis of |
GSM923442 |
| Reanalysis of |
GSM923443 |
| Reanalysis of |
GSM923444 |
| Reanalysis of |
GSM923445 |
| Reanalysis of |
GSM923446 |
| Reanalysis of |
GSM923447 |
| Reanalysis of |
GSM923448 |
| Reanalysis of |
GSM923449 |
| Reanalysis of |
GSM923450 |
| Reanalysis of |
GSM923451 |
| Reanalysis of |
GSM923452 |
| Reanalysis of |
GSM923453 |
| BioProject |
PRJNA234285 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE53984_GSM923439_Gm12812_Rep1_segments.bed.gz |
11.5 Kb |
(ftp)(http) |
BED |
| GSE53984_GSM923440_Gm12801_Rep1_segments.bed.gz |
10.8 Kb |
(ftp)(http) |
BED |
| GSE53984_GSM923441_Sknsh_Rep1_segments.bed.gz |
6.7 Kb |
(ftp)(http) |
BED |
| GSE53984_GSM923442_Mcf7_Rep1_segments.bed.gz |
11.6 Kb |
(ftp)(http) |
BED |
| GSE53984_GSM923443_Gm06990_Rep1_segments.bed.gz |
11.4 Kb |
(ftp)(http) |
BED |
| GSE53984_GSM923444_Bj_Rep1_segments.bed.gz |
14.2 Kb |
(ftp)(http) |
BED |
| GSE53984_GSM923444_Bj_Rep2_segments.bed.gz |
12.7 Kb |
(ftp)(http) |
BED |
| GSE53984_GSM923445_Nhek_Rep1_segments.bed.gz |
14.5 Kb |
(ftp)(http) |
BED |
| GSE53984_GSM923446_Hepg2_Rep1_segments.bed.gz |
11.5 Kb |
(ftp)(http) |
BED |
| GSE53984_GSM923447_Imr90_Rep1_segments.bed.gz |
13.2 Kb |
(ftp)(http) |
BED |
| GSE53984_GSM923448_K562_Rep1_segments.bed.gz |
12.3 Kb |
(ftp)(http) |
BED |
| GSE53984_GSM923449_Helas3_Rep1_segments.bed.gz |
15.3 Kb |
(ftp)(http) |
BED |
| GSE53984_GSM923450_Gm12813_Rep1_segments.bed.gz |
11.2 Kb |
(ftp)(http) |
BED |
| GSE53984_GSM923451_Gm12878_Rep1_segments.bed.gz |
11.0 Kb |
(ftp)(http) |
BED |
| GSE53984_GSM923452_Huvec_Rep1_segments.bed.gz |
15.9 Kb |
(ftp)(http) |
BED |
| GSE53984_GSM923453_Bg02es_Rep1_segments.bed.gz |
21.5 Kb |
(ftp)(http) |
BED |
| Processed data are available on Series record |
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