research-article

Decoding dendritic cell function through module and network analysis

Authors:

Gaurav Pandey,

Ariella Cohain,

Jennifer Miller,

Miriam MeradAuthors Info & Claims

BCB '12: Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine

Pages 627 - 628

https://doi.org/10.1145/2382936.2383047

Published: 07 October 2012 Publication History

Get Access

Abstract

Dendritic cells (DCs) serve as the sentinels of the immune system by informing the system about external stimuli, based on which an adaptive response can be mounted. However, not much is known about the genes and their interactions that regulate DC function. Using a large gene expression compendium, we uncover promising regulatory networks underlying the functioning of DCs and their subsets.

References

[1]

Banchereau, J. and Steinman, R. M. Dendritic cells and the control of immunity. Nature, 392, 6673 (Mar 19 1998), 245--252.

Google Scholar

[2]

Miller, J. C. et al. Deciphering the transcriptional network of the dendritic cell lineage. Nat Immunol(Jul 15 2012).

Google Scholar

[3]

Hildner, K. et al. Batf3 deficiency reveals a critical role for CD8alpha+ dendritic cells in cytotoxic T cell immunity. Science, 322, 5904 (Nov 14 2008), 1097--1100.

Google Scholar

[4]

Satpathy, A. T. et al. Zbtb46 expression distinguishes classical dendritic cells and their committed progenitors from other immune lineages. J Exp Med, 209, 6 (Jun 4 2012), 1135--1152.

Crossref

Google Scholar

[5]

Novershtern, N. et al. Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell, 144, 2 (Jan 21 2011), 296--309.

Crossref

Google Scholar

[6]

Heng, T. S. and Painter, M. W. The Immunological Genome Project: networks of gene expression in immune cells. Nat Immunol, 9, 10 (Oct 2008), 1091--1094.

Crossref

Google Scholar

[7]

Langfelder, P. and Horvath, S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics, 92008), 559.

Google Scholar

[8]

Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A, 102, 43 (Oct 25 2005), 15545--15550.

Crossref

Google Scholar

[9]

Botelho, R. J. et al. Localized diacylglycerol-dependent stimulation of Ras and Rap1 during phagocytosis. J Biol Chem, 284, 42 (Oct 16 2009), 28522--28532.

Crossref

Google Scholar

[10]

Huber, C. et al. FGD2, a CDC42-specific Exchange Factor Expressed by Antigen-presenting Cells, Localizes to Early Endosomes and Active Membrane Ruffles. Journal of Biological Chemistry, 283, 49 2008), 34002--34012.

Crossref

Google Scholar

Index Terms

Decoding dendritic cell function through module and network analysis
1. Applied computing
  1. Life and medical sciences
2. Information systems
  1. Information systems applications
    1. Data mining

Recommendations

A survey of disease connections for CD4+ T cell master genes and their directly linked genes

HighlightsCD4+ T cell subtype master genes and their connected genes are more likely to be associated with a disease or a phenotype.Genes connected to the CD4+ T cell subtype master genes are more likely to be transcription factors.CD4+ T cell subtype ...
Integrated pathway-based transcription regulation network mining and visualization based on gene expression profiles

Display Omitted An integrated pathway-oriented method is proposed for analyzing transcription regulation networks from gene expression data.The method currently is based on KEGG pathway definitions but is flexible to other pathway models.This improves ...
CanMod: A computational model to identify co-regulatory modules in cancer
BCB '20: Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics

Transcription factors (TFs) and microRNAs (miRNAs) are two important classes of gene regulators that govern many critical biological processes. Dysregulation of TF-gene and miRNA-gene interactions can lead to the development of multiple diseases ...

Comments

Information & Contributors

Information

Published In

BCB '12: Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine

October 2012

725 pages

ISBN:9781450316705

DOI:10.1145/2382936

General Chair:
Sanjay Ranka
University of Florida
,
Program Chairs:
Tamer Kahveci
University of Florida
,
Mona Singh
Princeton University

Publisher

Association for Computing Machinery

New York, NY, United States

Publication History

Published: 07 October 2012

Permissions

Request permissions for this article.

Request Permissions

Check for updates

Author Tags

Qualifiers

Research-article

Conference

BCB' 12

Sponsor:

SIGBio

BCB' 12: ACM International Conference on Bioinformatics, Computational Biology and Biomedicine

October 7 - 10, 2012

Florida, Orlando

Acceptance Rates

BCB '12 Paper Acceptance Rate 33 of 159 submissions, 21%;

Overall Acceptance Rate 254 of 885 submissions, 29%

Other Metrics

View Article Metrics

Bibliometrics & Citations

Bibliometrics

Article Metrics

0
Total Citations
69
Total Downloads

Downloads (Last 12 months)4
Downloads (Last 6 weeks)0

Reflects downloads up to 05 Mar 2025

Other Metrics

View Author Metrics

Citations

View Options

Login options

Check if you have access through your login credentials or your institution to get full access on this article.

Full Access

Get this Publication

View options

PDF

View or Download as a PDF file.

PDF

eReader

View online with eReader.

eReader

Abstract

References

Index Terms

Recommendations

A survey of disease connections for CD4+ T cell master genes and their directly linked genes

Integrated pathway-based transcription regulation network mining and visualization based on gene expression profiles

CanMod: A computational model to identify co-regulatory modules in cancer

Comments

Information

Published In

Sponsors

Publisher

Publication History

Permissions

Check for updates

Author Tags

Qualifiers

Conference

Acceptance Rates

Contributors

Other Metrics

Bibliometrics

Article Metrics

Other Metrics

Citations

Login options

Full Access

View options

PDF

eReader

Share

Share this Publication link

Share on social media

Affiliations