An Extension of Weighted Gene Co-Expression Network Analysis to Include Signed Interactions

Feb 16, 2013

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An Extension of Weighted Gene Co-Expression Network Analysis to Include Signed Interactions

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Beyond Co-expression: Gene Network Inference

Beyond Co-expression: Gene Network Inference. Patrik D’haeseleer Harvard University http:/genetics.med.harvard.edu/~patrik. Beyond Co-expression. Clustering approaches rely on co-expression of genes under different conditions Assumes co-expression is caused by co-regulation

952 views • 56 slides

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

ES cell culture . Self- renewing. Endoderm. Ecto- derm. Meso- derm. Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells. Steve Horvath University of California, Los Angeles Acknowledgement: Dissertation work of Mike J Mason

632 views • 36 slides

Extended Overview of Weighted Gene Co-Expression Network Analysis (WGCNA)

Extended Overview of Weighted Gene Co-Expression Network Analysis (WGCNA). Steve Horvath University of California, Los Angeles. Book on weighted networks. E-book is often freely accessible if the library has a subscription to Springer books. Contents.

1.9k views • 73 slides

Analysis of Gene Expression - Overview -

Analysis of Gene Expression - Overview -. Julia Paxson DVM DACVIM. Why gene expression analysis?. Quantification of mRNA transcript abundance High specificity, +/- high through-put Requires sequence knowledge. Considerations. Experimental question Species limitations

368 views • 13 slides

Detecting Network Motifs in Gene Co-expression Networks

Detecting Network Motifs in Gene Co-expression Networks. Shahar Artzi. Outline. Introduction to Network Motifs Introduction to Detecting Network Motifs Co-expression Network Network Motif Discovery Scale-Free Networks Result Discussion. Network Motifs. What is “Network Motifs” ?

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Analysis of Gene Expression Data

Analysis of Gene Expression Data. Rainer Breitling r.breitling@bio.gla.ac.uk Bioinformatics Research Centre and Institute of Biomedical and Life Sciences University of Glasgow. Outline. Gene expression biology Measuring gene expression levels

977 views • 60 slides

An Overview of Weighted Gene Co-Expression Network Analysis

An Overview of Weighted Gene Co-Expression Network Analysis. Steve Horvath University of California, Los Angeles. Contents. How to construct a weighted gene co-expression network? Why use soft thresholding? How to detect network modules? How to relate modules to an external clinical trait?

742 views • 51 slides

Extended Overview of Weighted Gene Co-Expression Network Analysis (WGCNA)

Extended Overview of Weighted Gene Co-Expression Network Analysis (WGCNA). Steve Horvath University of California, Los Angeles. Webpage where the material can be found. http:// www.genetics.ucla.edu /labs/ horvath / CoexpressionNetwork /WORKSHOP/

1.43k views • 103 slides

Serial Analysis of Gene Expression

Serial Analysis of Gene Expression. Velculescu, V., Zhang, L., Vogelstein, B. Kinzler, K. (1995) Science. Authors: The Wild-Types. Victor Velculescu: Keyboard Ken Kinzler Drummer Bert Vogelstein Keyboard Lin Zhang Honorary member. Current Research.

853 views • 22 slides

Gene Expression Analysis

Gene Expression Analysis. Benny Shomer January 2006. Whole in situ hybridization with the myeloid-specific marker, lysozyme C. NOTE!!! Studying a static RNA expression level is far from providing the ultimate answer!.

1.42k views • 97 slides

Network Construction “A General Framework for Weighted Gene Co-Expression Network Analysis”

Network Construction “A General Framework for Weighted Gene Co-Expression Network Analysis”. Steve Horvath Human Genetics and Biostatistics University of CA, LA. Background. Network based methods have been found useful in many domains, protein interaction networks the world wide web

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A General Framework for Weighted Gene Co-Expression Network Analysis

A General Framework for Weighted Gene Co-Expression Network Analysis. Steve Horvath Human Genetics and Biostatistics University of CA, LA. Content. Novel statistical approach for analyzing microarray data: weighted gene co-expression network analysis

1.07k views • 62 slides

A Geometric Interpretation of Gene Co-Expression Network Analysis Steve Horvath, Jun Dong

A Geometric Interpretation of Gene Co-Expression Network Analysis Steve Horvath, Jun Dong. Outline. Network and network concepts Approximately factorizable networks Gene Co-expression Network Eigengene Factorizability, Eigengene Conformity Eigengene-based network concepts

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Protein/DNA Interactions and Gene Expression

Protein/DNA Interactions and Gene Expression. Michael J. Pikaart Assistant Professor Chemistry pikaart@hope.edu. Photograph. B.S., Calvin College, 1986 Ph.D., University of Michigan, 1992. Areas of expertise: Biochemistry, Transcription regulation, Chromatin structure. Grants and awards

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Differential Weighted Gene Coexpression Network Analysis Applied to Mouse Weight

Differential Weighted Gene Coexpression Network Analysis Applied to Mouse Weight. Tova Fuller Steve Horvath Department of Human Genetics University of California, Los Angeles ICSB, 10/5/07. Outline. Introduction: Single versus differential network analysis

312 views • 19 slides

Gene expression analysis

Gene expression analysis. Hyunju Lee School of Information and Communications. From Campbell and Heyer, “Discovering genomics, proteomics, & Bioinformatics,” , 2 nd ed.,wileylss.

1.1k views • 63 slides

Gene Expression Analysis

Gene Expression Analysis. Gene Expression. protein. RNA. DNA. Gene Expression. AAAAAAA. AAAAAAA. AAAAAAA. AAAAAAA. AAAAAAA. AAAAAAA. AAAAAAA. AAAAAAA. AAAAAAA. mRNA gene1. AAAAAAA. AAAAAAA. AAAAAAA. AAAAAAA. AAAAAAA. mRNA gene2. AAAAAAA. AAAAAAA. AAAAAAA. AAAAAAA.

539 views • 38 slides

Gene Expression Analysis

Gene Expression Analysis. Benny Shomer January 2005. Whole in situ hybridization with the myeloid-specific marker, lysozyme C. NOTE!!! Studying a static RNA expression level is far from providing the ultimate answer!.

1.08k views • 83 slides

Weighted Gene Co-Expression Network Analysis of Multiple Independent Lung Cancer Data Sets

Weighted Gene Co-Expression Network Analysis of Multiple Independent Lung Cancer Data Sets . Steve Horvath University of California, Los Angeles. Contents. Mini review of weighted correlation network analysis (WGCNA) Module preservation statistics Application to multiple adenocarcinoma.

965 views • 74 slides

RNA processing and regulation Network interactions in gene expression

Topics. RNA processing and regulation Network interactions in gene expression RASL-DASL the genome: approaches for systems biology. rRNA Processing Pathway: Involvement of A Series of Endo- and Exonucleases. 18S. 5S. 28S. 45S. 41S. 32S. 20S. 5S. 28S. 18S. Maturation of tRNAs.

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A Geometric Interpretation of Gene Co-Expression Network Analysis Steve Horvath, Jun Dong

563 views • 53 slides

Gene Expression Analysis

BI420 – Introduction to Bioinformatics. Gene Expression Analysis. Gabor T. Marth. Department of Biology, Boston College marth@bc.edu. Gene expression. Why study gene expression?. Which genes are active. at different developmental stages? in cells of different tissues?

415 views • 30 slides

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