2016-07-14T19:01:14Z

Bouhassi: /* GenPlay Project */

This page contains GenPlay projects available for download. These projects illustrate the type of data analysis and visualization that can be done with GenPlay.
There are two sections: the first one contains projects that were used as supporting data of published articles. The second section contains the projects created for the [[Tutorials]] page of this website.

== How to start a project ==
You first need to download and install GenPlay from the [[Downloads]] page.
Then, you need to download the project you want to launch. Once the download is finished, double click on the project file to start GenPlay and load the project. Loading a project might take a few minutes.

== Projects from published work ==
=== GenPlay Multi-Genome, a tool to compare and analyze multiple human genomes in a graphical interface ===
====Authors====
Julien Lajugie, Nicolas Fourel and Eric E Bouhassira
====Abstract====
The number of human genomes sequenced is growing exponentially. The vast majority of these genomes are assembled by comparison to a single reference sequence. This is problematic because of the large amount of genetic variations in human populations. Parallel analysis and visualization of the indels and structural variants present in multiple human genomes is complex because it requires the display of sequences that are unique to specific genomes and absent from the reference sequence. We describe here, GenPlay Multi-Genome, an application that can be used to visualize SNPs, indels and structural variants in multiple human genomes. GenPlay Multi-Genome is ideal for the comparison in a graphic interface of expression and epigenetic data obtained from multiple phased genomes. GenPlay Multi- Genome is also useful to analyze data that has been aligned to custom genomes rather than to a reference genome.
====Article====
[http://bioinformatics.oxfordjournals.org/content/31/1/109.long http://bioinformatics.oxfordjournals.org/content/31/1/109.long]

====GenPlay Project====
[http://genplay.einstein.yu.edu/library/projects/GenPlay_MG_2014/MG_Demo.zip MG_Demo.zip]

'''Note:''' Uncompress the zip file and double click on MG_demo.gppf to start GenPlay (make sure that GenPlay is installed on your system).

----

=== Allele-Specific Genome-wide Profiling in Human Primary Erythroblasts Reveal Replication Program Organization ===
====Authors====
Rituparna Mukhopadhyay, Julien Lajugie, Nicolas Fourel, Ari Selzer, Michael Schizas, Boris Bartholdy, Jessica Mar, Chii Mei Lin, Melvenia M. Martin, Michael Ryan, Mirit I. Aladjem and Eric E. Bouhassira
====Abstract====
We have developed a new approach based on TimEX-seq to characterize allele-specific timing of DNA replication genome-wide in human primary basophilic erythroblasts. We show that the two chromosome homologs replicate at the same time in about 88% of the genome and that large structural variants are preferentially associated with asynchronously replications. We identified about 600 megabase-sized asynchronously replicated domains in two tested individuals. We show that the longest asynchronously replicated domains are enriched in imprinted genes suggesting that structural variants and parental imprinting are two causes of replication asynchrony in the human genome. Biased chromosome X inactivation in one of the two individuals tested was another source of detectable replication asynchrony. Analysis of high-resolution TimEX profiles revealed timing wrinkles, which are previously undetected, highly reproducible, variations of the timing of replication in the 100kb-range that exist within the well-characterized megabase-sized replication timing domains. We show that these wrinkles correspond to clusters of origins of replication that we detected using novel nascent strands DNA profiling methods. Analysis of the distribution of replication origins revealed dramatic differences in initiation of replication frequency during S phase and a strong association, in both synchronous and asynchronous regions, between origins of replication and three genomic features: G-quadruplexes, CpG Islands and transcription start sites. The frequency of initiation in asynchronous regions was similar in the two homologs. Asynchronous regions were richer in origins of replication than synchronous regions.
====Article====
[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004319 http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004319]

====GenPlay Project====
[http://genplay.einstein.yu.edu/library/projects/TimEX-NascentStrands-2013/Timing_and_NS_Profiles_2013.gppf Timing_and_NS_Profiles_2013.gppf]

----

=== Allele-specific analysis of DNA replication origins in mammalian cells===
====Authors====
Bartholdy B, Mukhopadhyay R, Lajugie J, Aladjem MI, Bouhassira EE
====Abstract====
The mechanisms that control the location and timing of firing of replication origins are poorly understood. Using a novel functional genomic approach based on the analysis of SNPs and indels in phased human genomes, we observe that replication asynchrony is associated with small cumulative variations in the initiation efficiency of multiple origins between the chromosome homologues, rather than with the activation of dormant origins. Allele-specific measurements demonstrate that the presence of G-quadruplex-forming sequences does not correlate with the efficiency of initiation. Sequence analysis reveals that the origins are highly enriched in sequences with profoundly asymmetric G/C and A/T nucleotide distributions and are almost completely depleted of antiparallel triplex-forming sequences. We therefore propose that although G4-forming sequences are abundant in replication origins, an asymmetry in nucleotide distribution, which increases the propensity of origins to unwind and adopt non-B DNA structure, rather than the ability to form G4, is directly associated with origin activity.

====Article====
[http://www.ncbi.nlm.nih.gov/pubmed/25987481]

====GenPlay Project====
[http://genplay.einstein.yu.edu/library/projects/Allele_Specific_NS_Sequencing_FNY01_2_2/FNY01_2_2_allele_specific_analysis_of_replication_origins_hg19.gppf]

[http://genplay.einstein.yu.edu/library/projects/Allele_Specific_NS_Sequencing_FNY01_2_2/readme_for_FNY01_2_2_AS_analysis_of_replication_origin_gppf.txt readme_for_FNY01_2_2_AS_analysis_of_replication_origin_gppf.txt]

----

=== Identification of a BET Family Bromodomain/Casein Kinase II/TAF-Containing Complex as a Regulator of Mitotic Condensin Function ===
====Authors====
Hyun-Soo Kim, Rituparna Mukhopadhyay, Scott B. Rothbart, Andrea C. Silva, Vincent Vanoosthuyse, Ernest Radovani, Thomas Kislinger, Assen Roguev, Colm J. Ryan, Jiewei Xu, Harlizawati Jahari, Kevin G. Hardwick, Jack F. Greenblatt, Nevan J. Krogan, Jeffrey S. Fillingham, Brian D. Strahl, Eric E. Bouhassira, Winfried Edelmann, Michael-Christopher Keogh
====Abstract====
Condensin is a central regulator of mitotic genome structure with mutants showing poorly condensed chromosomes and profound segregation defects. Here, we identify NCT, a complex comprising the Nrc1 BET-family tandem bromodomain protein (SPAC631.02), casein kinase II (CKII), and several TAFs, as a regulator of condensin function. We show that NCT and condensin bind similar genomic regions but only briefly colocalize during the periods of chromosome condensation and decondensation. This pattern of NCT binding at the core centromere, the region of maximal condensin enrichment, tracks the abundance of acetylated histone H4, as regulated by the Hat1-Mis16 acetyltransferase complex and recognized by the first Nrc1 bromodomain. Strikingly, mutants in NCT or Hat1-Mis16 restore the formation of segregation-competent chromosomes in cells containing defective condensin. These results are consistent with a model where NCT targets CKII to chromatin in a cell-cycle-directed manner in order to modulate the activity of condensin during chromosome condensation and decondensation.
====Article====
[http://www.cell.com/cell-reports/fulltext/S2211-1247(14)00063-1 http://www.cell.com/cell-reports/fulltext/S2211-1247(14)00063-1]
====GenPlay Project====
[http://genplay.einstein.yu.edu/library/projects/CellReports-2014/Kim_CellRep_2014.gppf Kim_CellRep_2014.gppf]

----

=== Methylation ===
Submitted for publication
====Authors====
Boris Bartholdy, Julien Lajugie, Rituparna Mukhopadhyay, John M Greally, Masako Suzuki and Eric E Bouhassira

====Abstract====
Submitted for publication
====Article====
Submitted for publication
====GenPlay Project====

[http://genplay.einstein.yu.edu/library/projects/Methylation_2016/Methyl_seq_paper_figure_1.gppf Methyl_seq_paper_figure_1.gppf]

[http://genplay.einstein.yu.edu/library/projects/Methylation_2016/3_2_3_3_AS_methylation_data.gppf 3_2_3_3_AS_methylation_data.gppf]

== Projects from tutorials ==
===ChIP-Seq Tutorial===
====Goal====
The objective of the ChIP-Seq tutorial is to illustrate how GenPlay can be used to isolate peaks from the data generated from a ChIP-Seq experiment. Then, to generate a list of genes that have a peak in their promoter and finally to associate the score of the peak summit with each promoter.

====Tutorial====
[[ChIP-Seq Tutorial]]

====Project File====
[http://genplay.einstein.yu.edu/library/tutorials/ChIP-Seq/ChIP-Seq_Tutorial.gppf ChIP-Seq_Tutorial.gppf]

----

=== TimEX Tutorial===
====Goal====
The TimEX tutorial illustrates how GenPlay can be used to show timing of replication profiles. The goal of the tutorial is to compute the correlation coefficient between the replication timing in human embryonic stem (ES) cells and in primary basophilic erythroblasts derived in culture from primary CD34 positive cells.
====Tutorial====
[[TimEX Tutorial]]
====Project File====
[http://genplay.einstein.yu.edu/library/tutorials/TimEX/TimEX_Tutorial.gppf TimEX_Tutorial.gppf]

----

=== Multi-Genome Tutorial===

====Goal====
The multi-genome tutorial explains how to display data mapped on genome assembly GRCh37/Hg19 and GRCh38/Hg38 simultaneously.

====Tutorial====
[[GRCh37/hg19 GRCh38/hg38 Multi-Genome Tutorial]]

'''Note:''' An older version of this tutorial is available for NCBI36/hg18 - GRCh37/hg19: [[Multi-Genome Tutorial]]

====Project File====
[http://genplay.einstein.yu.edu/library/tutorials//MG-hg38-hg19/hg19-hg38_Multi-genome.zip hg19-hg38_Multi-genome.zip]

'''Note:''' To start the project you need to unpack the zip archive and to double click on the file called ''hg19-hg38_Multi-genome.gppf''. Make sure that GenPlay is installed on your computer.

'''Note2:''' For the NCBI36/hg18 - GRCh37/hg19 version, click on the following link: [http://genplay.einstein.yu.edu/library/tutorials/MG-Reference_Genome_Tutorial/GenPlayMG-Reference_Genome_Tutorial.zip GenPlayMG-Reference_Genome_Tutorial.zip]. To start the project you need to unpack the zip archive and to double click on the file called ''GenPlay-MG – Reference genome tutorial.gppf''. Make sure that GenPlay is installed on your computer.

Projects

2016-07-14T18:59:00Z

Bouhassi: /* GenPlay Project */

This page contains GenPlay projects available for download. These projects illustrate the type of data analysis and visualization that can be done with GenPlay.
There are two sections: the first one contains projects that were used as supporting data of published articles. The second section contains the projects created for the [[Tutorials]] page of this website.

== How to start a project ==
You first need to download and install GenPlay from the [[Downloads]] page.
Then, you need to download the project you want to launch. Once the download is finished, double click on the project file to start GenPlay and load the project. Loading a project might take a few minutes.

== Projects from published work ==
=== GenPlay Multi-Genome, a tool to compare and analyze multiple human genomes in a graphical interface ===
====Authors====
Julien Lajugie, Nicolas Fourel and Eric E Bouhassira
====Abstract====
The number of human genomes sequenced is growing exponentially. The vast majority of these genomes are assembled by comparison to a single reference sequence. This is problematic because of the large amount of genetic variations in human populations. Parallel analysis and visualization of the indels and structural variants present in multiple human genomes is complex because it requires the display of sequences that are unique to specific genomes and absent from the reference sequence. We describe here, GenPlay Multi-Genome, an application that can be used to visualize SNPs, indels and structural variants in multiple human genomes. GenPlay Multi-Genome is ideal for the comparison in a graphic interface of expression and epigenetic data obtained from multiple phased genomes. GenPlay Multi- Genome is also useful to analyze data that has been aligned to custom genomes rather than to a reference genome.
====Article====
[http://bioinformatics.oxfordjournals.org/content/31/1/109.long http://bioinformatics.oxfordjournals.org/content/31/1/109.long]

====GenPlay Project====
[http://genplay.einstein.yu.edu/library/projects/GenPlay_MG_2014/MG_Demo.zip MG_Demo.zip]

'''Note:''' Uncompress the zip file and double click on MG_demo.gppf to start GenPlay (make sure that GenPlay is installed on your system).

----

=== Allele-Specific Genome-wide Profiling in Human Primary Erythroblasts Reveal Replication Program Organization ===
====Authors====
Rituparna Mukhopadhyay, Julien Lajugie, Nicolas Fourel, Ari Selzer, Michael Schizas, Boris Bartholdy, Jessica Mar, Chii Mei Lin, Melvenia M. Martin, Michael Ryan, Mirit I. Aladjem and Eric E. Bouhassira
====Abstract====
We have developed a new approach based on TimEX-seq to characterize allele-specific timing of DNA replication genome-wide in human primary basophilic erythroblasts. We show that the two chromosome homologs replicate at the same time in about 88% of the genome and that large structural variants are preferentially associated with asynchronously replications. We identified about 600 megabase-sized asynchronously replicated domains in two tested individuals. We show that the longest asynchronously replicated domains are enriched in imprinted genes suggesting that structural variants and parental imprinting are two causes of replication asynchrony in the human genome. Biased chromosome X inactivation in one of the two individuals tested was another source of detectable replication asynchrony. Analysis of high-resolution TimEX profiles revealed timing wrinkles, which are previously undetected, highly reproducible, variations of the timing of replication in the 100kb-range that exist within the well-characterized megabase-sized replication timing domains. We show that these wrinkles correspond to clusters of origins of replication that we detected using novel nascent strands DNA profiling methods. Analysis of the distribution of replication origins revealed dramatic differences in initiation of replication frequency during S phase and a strong association, in both synchronous and asynchronous regions, between origins of replication and three genomic features: G-quadruplexes, CpG Islands and transcription start sites. The frequency of initiation in asynchronous regions was similar in the two homologs. Asynchronous regions were richer in origins of replication than synchronous regions.
====Article====
[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004319 http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004319]

====GenPlay Project====
[http://genplay.einstein.yu.edu/library/projects/TimEX-NascentStrands-2013/Timing_and_NS_Profiles_2013.gppf Timing_and_NS_Profiles_2013.gppf]

----

=== Allele-specific analysis of DNA replication origins in mammalian cells===
====Authors====
Bartholdy B, Mukhopadhyay R, Lajugie J, Aladjem MI, Bouhassira EE
====Abstract====
The mechanisms that control the location and timing of firing of replication origins are poorly understood. Using a novel functional genomic approach based on the analysis of SNPs and indels in phased human genomes, we observe that replication asynchrony is associated with small cumulative variations in the initiation efficiency of multiple origins between the chromosome homologues, rather than with the activation of dormant origins. Allele-specific measurements demonstrate that the presence of G-quadruplex-forming sequences does not correlate with the efficiency of initiation. Sequence analysis reveals that the origins are highly enriched in sequences with profoundly asymmetric G/C and A/T nucleotide distributions and are almost completely depleted of antiparallel triplex-forming sequences. We therefore propose that although G4-forming sequences are abundant in replication origins, an asymmetry in nucleotide distribution, which increases the propensity of origins to unwind and adopt non-B DNA structure, rather than the ability to form G4, is directly associated with origin activity.

====Article====
[http://www.ncbi.nlm.nih.gov/pubmed/25987481]

====GenPlay Project====
[http://genplay.einstein.yu.edu/library/projects/Allele_Specific_NS_Sequencing_FNY01_2_2/FNY01_2_2_allele_specific_analysis_of_replication_origins_hg19.gppf FNY01_2_2_allele_specific_analysis_of _replication_origins_hg19.gppf]

[http://genplay.einstein.yu.edu/library/projects/Allele_Specific_NS_Sequencing_FNY01_2_2/readme_for_FNY01_2_2_AS_analysis_of_replication_origin_gppf.txt readme_for_FNY01_2_2_AS_analysis_of_replication_origin_gppf.txt]

----

=== Identification of a BET Family Bromodomain/Casein Kinase II/TAF-Containing Complex as a Regulator of Mitotic Condensin Function ===
====Authors====
Hyun-Soo Kim, Rituparna Mukhopadhyay, Scott B. Rothbart, Andrea C. Silva, Vincent Vanoosthuyse, Ernest Radovani, Thomas Kislinger, Assen Roguev, Colm J. Ryan, Jiewei Xu, Harlizawati Jahari, Kevin G. Hardwick, Jack F. Greenblatt, Nevan J. Krogan, Jeffrey S. Fillingham, Brian D. Strahl, Eric E. Bouhassira, Winfried Edelmann, Michael-Christopher Keogh
====Abstract====
Condensin is a central regulator of mitotic genome structure with mutants showing poorly condensed chromosomes and profound segregation defects. Here, we identify NCT, a complex comprising the Nrc1 BET-family tandem bromodomain protein (SPAC631.02), casein kinase II (CKII), and several TAFs, as a regulator of condensin function. We show that NCT and condensin bind similar genomic regions but only briefly colocalize during the periods of chromosome condensation and decondensation. This pattern of NCT binding at the core centromere, the region of maximal condensin enrichment, tracks the abundance of acetylated histone H4, as regulated by the Hat1-Mis16 acetyltransferase complex and recognized by the first Nrc1 bromodomain. Strikingly, mutants in NCT or Hat1-Mis16 restore the formation of segregation-competent chromosomes in cells containing defective condensin. These results are consistent with a model where NCT targets CKII to chromatin in a cell-cycle-directed manner in order to modulate the activity of condensin during chromosome condensation and decondensation.
====Article====
[http://www.cell.com/cell-reports/fulltext/S2211-1247(14)00063-1 http://www.cell.com/cell-reports/fulltext/S2211-1247(14)00063-1]
====GenPlay Project====
[http://genplay.einstein.yu.edu/library/projects/CellReports-2014/Kim_CellRep_2014.gppf Kim_CellRep_2014.gppf]

----

=== Methylation ===
Submitted for publication
====Authors====
Boris Bartholdy, Julien Lajugie, Rituparna Mukhopadhyay, John M Greally, Masako Suzuki and Eric E Bouhassira

====Abstract====
Submitted for publication
====Article====
Submitted for publication
====GenPlay Project====

[http://genplay.einstein.yu.edu/library/projects/Methylation_2016/Methyl_seq_paper_figure_1.gppf Methyl_seq_paper_figure_1.gppf]

[http://genplay.einstein.yu.edu/library/projects/Methylation_2016/3_2_3_3_AS_methylation_data.gppf 3_2_3_3_AS_methylation_data.gppf]

== Projects from tutorials ==
===ChIP-Seq Tutorial===
====Goal====
The objective of the ChIP-Seq tutorial is to illustrate how GenPlay can be used to isolate peaks from the data generated from a ChIP-Seq experiment. Then, to generate a list of genes that have a peak in their promoter and finally to associate the score of the peak summit with each promoter.

====Tutorial====
[[ChIP-Seq Tutorial]]

====Project File====
[http://genplay.einstein.yu.edu/library/tutorials/ChIP-Seq/ChIP-Seq_Tutorial.gppf ChIP-Seq_Tutorial.gppf]

----

=== TimEX Tutorial===
====Goal====
The TimEX tutorial illustrates how GenPlay can be used to show timing of replication profiles. The goal of the tutorial is to compute the correlation coefficient between the replication timing in human embryonic stem (ES) cells and in primary basophilic erythroblasts derived in culture from primary CD34 positive cells.
====Tutorial====
[[TimEX Tutorial]]
====Project File====
[http://genplay.einstein.yu.edu/library/tutorials/TimEX/TimEX_Tutorial.gppf TimEX_Tutorial.gppf]

----

=== Multi-Genome Tutorial===

====Goal====
The multi-genome tutorial explains how to display data mapped on genome assembly GRCh37/Hg19 and GRCh38/Hg38 simultaneously.

====Tutorial====
[[GRCh37/hg19 GRCh38/hg38 Multi-Genome Tutorial]]

'''Note:''' An older version of this tutorial is available for NCBI36/hg18 - GRCh37/hg19: [[Multi-Genome Tutorial]]

====Project File====
[http://genplay.einstein.yu.edu/library/tutorials//MG-hg38-hg19/hg19-hg38_Multi-genome.zip hg19-hg38_Multi-genome.zip]

'''Note:''' To start the project you need to unpack the zip archive and to double click on the file called ''hg19-hg38_Multi-genome.gppf''. Make sure that GenPlay is installed on your computer.

'''Note2:''' For the NCBI36/hg18 - GRCh37/hg19 version, click on the following link: [http://genplay.einstein.yu.edu/library/tutorials/MG-Reference_Genome_Tutorial/GenPlayMG-Reference_Genome_Tutorial.zip GenPlayMG-Reference_Genome_Tutorial.zip]. To start the project you need to unpack the zip archive and to double click on the file called ''GenPlay-MG – Reference genome tutorial.gppf''. Make sure that GenPlay is installed on your computer.