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Series GSE53984 Query DataSets for GSE53984
Status Public on May 25, 2015
Title Identification of Replication Timing Domains Using DNN-HMM
Sample organism Homo sapiens
Experiment type Third-party reanalysis
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)

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.

Contributor(s) Shu W, Liu F
Citation(s) 26545821
Submission date Jan 10, 2014
Last update date Nov 23, 2015
Contact name Wenjie Shu
Organization name Beijing Institute of Radiation Medicine
Street address Taiping Road 27
City Beijing
ZIP/Postal code 100850
Country China
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

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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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