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Target audience: Biologists, Genomicists, Co... 

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Authors: Michelle Brazas 

RNA-seq Analysis 2014 Module 4 - Isoform discovery and alternative expression

Explore use of Cufflinks in reference annotation based transcript (RABT) assembly mode and ‘de novo’ assembly mode. Both modes require a reference genome sequence.
 

Scientific topics: RNA

Keywords: Alternative expression, Transcript isoforms

RNA-seq Analysis 2014 Module 3 - Expression and Differential Expression

Get FPKM style expression estimates using Cufflinks

        Perform differential expression analysis with Cuffdiff

        Perform summary analysis with CummeRbund

        Downstream interpretation of expression analysis (multiple testing, clustering, heatmaps, classification, pathway analysis, etc.)

 

Keywords: Differential expression, Transript expression

RNA-seq Analysis 2014 Module 2 - Alignment and Visualization

Use of Bowtie/TopHat

        ‘Regular mode’ vs. ‘Fusion mode’

        Introduction to the BAM format

        Basic manipulation of BAMs with samtools, etc.

        Visualization of RNA-seq alignments - IGV

        BAM read counting and determination of variant allele expression status
 

 

Keywords: Data visualization, Rna seq alignment

RNA-seq Analysis 2014 Module 1 - Introduction to RNA-seq Analysis

Basic introduction to biology of RNA-seq

        Experimental design considerations

        Commonly asked questions

        Data visualization using IGV

 

Keywords: Experimental design rna seq, Igv, Introduction rna seq analysis

Pathway and Network Analysis 2014 Module 6 - Gene Function Prediction

Functional association networks and gene function prediction

    Homology based prediction

    Guilt-by-association: GeneMANIA

Keywords: Functional association networks, Gene function prediction, Genemania

Pathway and Network Analysis 2014 Module 5 - Network Visualization

Introduction to network visualization

    Visualizing omics data on a network or pathway

    Active modules in Cytoscape

Keywords: Cytoscape, Network visualization

Pathway and Network Analysis 2014 Module 4 - Pathway and Network Analysis

Introduction to pathway and network analysis

    Basic network concepts

    Types of pathway and network information

    Pathway Databases: Reactome, KEGG, etc.

    Pathway analysis of large scale genomics data sets, including cancer genomics

Keywords: Biological networks, Kegg, Pathway analysis, Reactome

Pathway and Network Analysis 2014 Module 3 - Gene Regulation Analysis

Overview of transcription

    Data sources for regulatory data - Chromatin IP, DNA hypersensitivity, other chip data

    Basics of processing data

    Pattern discovery

Keywords: Pattern discovery, Transcriptional regulation

Pathway and Network Analysis 2014 Module 2 - Finding Over-represented Pathways

Over-representation analysis (ORA)

    Statistics for detecting over-representation e.g. hypergeometric test, GSEA

    Multiple testing correction: Bonferroni, Benjamini-Hochberg FDR

    Filtering Gene Ontology e.g. using evidence codes

Keywords: Gsea, Over representation analysis

Pathway and Network Analysis 2014 Module 1 - Introduction to Gene Lists

Gene list analysis overview: Workflow of concepts and tools from gene list to pathway analysis

    Where do gene lists come from?

    Working with gene function information

Keywords: Gene lists, Gene ontology