NDLI: Regression hidden Markov modeling reveals heterogeneous gene expression regulation: a case study in mouse embryonic stem cells

Content Provider	Springer Nature : BioMed Central
Author	Lee, Yeonok Ghosh, Debashis Zhang, Yu
Abstract	Background Studies have shown the strong association between histone modification levels and gene expression levels. The detailed relationships between the two can vary substantially due to differential regulation, and hence a simple regression model may not be adequate. We apply a regression hidden Markov model (regHMM) to further investigate the potential multiple relationships between genes and histone methylation levels in mouse embryonic stem cells. Results Seven histone methylation levels are used in the study. Averaged histone modifications over non-overlapping 200 bp windows on the range transcription starting site (TSS) ± 1 Kb are used as predictors, and in total 70 explanatory variables are generated. Based on regHMM results, genes segregated into two groups, referred to as State 1 and State 2, have distinct association strengths. Genes in State 1 are better explained by histone methylation levels with R2=.72 while those in State 2 have weaker association strength with R2=.38. The regression coefficients in the two states are not very different in magnitude except in the intercept,.25 and 1.15 for State 1 and State 2, respectively. We found specific GO categories that may be attributed to the different relationships. The GO categories more frequently observed in State 2 match those of housekeeping genes, such as cytoplasm, nucleus, and protein binding. In addition, the housekeeping gene expression levels are significantly less explained by histone methylation in mouse embryonic stem cells, which is consistent with the constitutive expression patterns that would be expected. Conclusion Gene expression levels are not universally affected by histone methylation levels, and the relationships between the two differ by the gene functions. The expression levels of the genes that perform the most common housekeeping genes’ GO categories are less strongly associated with histone methylation levels. We suspect that additional biological factors may also be strongly associated with the gene expression levels in State 2. We discover that the effect of the presence of CpG island in TSS ± 1 Kb is larger in State 2.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/1471-2164-15-360.pdf
Ending Page	15
Page Count	15
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/1471-2164-15-360
Journal	BMC Genomics
Issue Number	1
Volume Number	15
Language	English
Publisher	BioMed Central
Publisher Date	2014-05-12
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Regression hidden Markov model Histone modification Gene expression level Mouse embryonic stem cell
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features

Regression hidden Markov modeling reveals heterogeneous gene expression regulation: a case study in mouse embryonic stem cells

Comparative analysis of expression of histone H2a genes in mouse

Gene function in early mouse embryonic stem cell differentiation

Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells

Smyd3, a histone methyltransferase, modulates the growth and differentiation of human cardiac stem cells

Transcriptome coexpression map of human embryonic stem cells

Searching ChIP-seq genomic islands for combinatorial regulatory codes in mouse embryonic stem cells

Detailed characterization of the mouse embryonic stem cell transcriptome reveals novel genes and intergenic splicing associated with pluripotency

Regression hidden Markov modeling reveals heterogeneous gene expression regulation: a case study in mouse embryonic stem cells

Similar Documents

Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features

Regression hidden Markov modeling reveals heterogeneous gene expression regulation: a case study in mouse embryonic stem cells

Comparative analysis of expression of histone H2a genes in mouse

Gene function in early mouse embryonic stem cell differentiation

Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells

Smyd3, a histone methyltransferase, modulates the growth and differentiation of human cardiac stem cells

Transcriptome coexpression map of human embryonic stem cells

Searching ChIP-seq genomic islands for combinatorial regulatory codes in mouse embryonic stem cells

Detailed characterization of the mouse embryonic stem cell transcriptome reveals novel genes and intergenic splicing associated with pluripotency

Regression hidden Markov modeling reveals heterogeneous gene expression regulation: a case study in mouse embryonic stem cells