Hierarchical clustering and principal component analysis of CpG methylation profiles obtained in the F1 reciprocal crosses. Article Swipe
Dacosta Michelle
,
Michael Mueller
,
Martyna Adamowicz‐Brice
,
J. Collins Melissa
,
Gellert Pascal
,
Klio Maratou
,
K. Srivastava Prashant
,
Rotival Maxime
,
Shahena Butt
,
Game Laurence
,
Satbhai Santosh
,
Silver Nicholas
,
J. Norsworthy Penny
,
R. Langley Sarah
,
Petretto Enrico
,
Pravenec Michal
,
Jeremy Timothy
·
YOU?
·
· 2015
· Open Access
·
· DOI: https://doi.org/10.1371/journal.pgen.1004813.g006
YOU?
·
· 2015
· Open Access
·
· DOI: https://doi.org/10.1371/journal.pgen.1004813.g006
Dendrograms showing the results of clustering the CpG methylation profiles obtained in each of the F1 animals before (A) and after (C) phasing the read data by parental genotype. The prefix of the phased F1 profiles in (C) denotes the reciprocal cross (bnxshr, shrxbn) and the suffix the genotype of the phased read set (bn = Brown Norway, shr = Spontaneously Hypertensive Rat). Numbers after the reciprocal cross prefix denote biological replicates. Profiles were clustered by the Ward's method using the pairwise euclidean distance between the profiles as the distance metric. Panels B and D show the projection of methylation profiles onto the 1st principal component (PC). Replicates for each cross-genotype combination are separated along the y-axis. The prefix of the label denotes the reciprocal cross (bnxshr, shrxbn), the suffix denotes the parental genotype (bn, shr). While the 1st PC does not separate crosses in the unphased data it provides complete separation by parental genotype in the phased data. Only CpGs with at least 5× coverage in each replicate/phased read set were included in the analysis and CpG positions affected by SNPs/indels were removed prior to clustering and principal component analysis.
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- Type
- paratext
- Language
- en
- Landing Page
- https://figshare.com/articles/figure/_Hierarchical_clustering_and_principal_component_analysis_of_CpG_methylation_profiles_obtained_in_the_F1_reciprocal_crosses_/1260341
- OA Status
- green
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W2196737602
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- OpenAlex ID
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https://openalex.org/W2196737602Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1371/journal.pgen.1004813.g006Digital Object Identifier
- Title
-
Hierarchical clustering and principal component analysis of CpG methylation profiles obtained in the F1 reciprocal crosses.Work title
- Type
-
paratextOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2015Year of publication
- Publication date
-
2015-12-02Full publication date if available
- Authors
-
Dacosta Michelle, Michael Mueller, Martyna Adamowicz‐Brice, J. Collins Melissa, Gellert Pascal, Klio Maratou, K. Srivastava Prashant, Rotival Maxime, Shahena Butt, Game Laurence, Satbhai Santosh, Silver Nicholas, J. Norsworthy Penny, R. Langley Sarah, Petretto Enrico, Pravenec Michal, Jeremy TimothyList of authors in order
- Landing page
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https://figshare.com/articles/figure/_Hierarchical_clustering_and_principal_component_analysis_of_CpG_methylation_profiles_obtained_in_the_F1_reciprocal_crosses_/1260341Publisher landing page
- Open access
-
YesWhether a free full text is available
- OA status
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greenOpen access status per OpenAlex
- OA URL
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https://figshare.com/articles/figure/_Hierarchical_clustering_and_principal_component_analysis_of_CpG_methylation_profiles_obtained_in_the_F1_reciprocal_crosses_/1260341Direct OA link when available
- Concepts
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Biology, Principal component analysis, CpG site, Reciprocal, Cluster analysis, DNA methylation, Hierarchical clustering, Genetics, Methylation, Component (thermodynamics), Evolutionary biology, Computational biology, Statistics, DNA, Gene, Mathematics, Gene expression, Physics, Philosophy, Thermodynamics, LinguisticsTop concepts (fields/topics) attached by OpenAlex
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10Other works algorithmically related by OpenAlex
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