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BIF-30806 Group Project Group (A)rabidopsis: David Nieuwenhuijse Matthew Price Qianqian Zhang Thijs Slijkhuis Species: C. Elegans Project: Advanced (+Basic) Progress Report Project Overview Dataset Preparation Transcriptome Construction Pipeline Differentially Expressed Genes Gene Function Biological Explanation Co-expressed Genes Modules Functional Description & Explanation Module Conservation b/w species Gene Expression (Basic Project) Relationship to Transcript Properties Visualisation of Interaction Network Results so far David Nieuwenhuijse ◦ GeneID and GO term extraction tool ◦ Cytoscape GO enrichment analysis ◦ Finding automatic GO enrichment tool for pipeline Qianqian Zhang ◦ Create shell script for running Cuffdiff, Gffread and Samtools program ◦ Get the gene lists of most differentially expressed genes and highest expressed genes ◦ Visualization of differentially expressed genes by cummeRbund package: Density plot, Scatter plot, Volcano plot, P value distribution plot, MA plot etc. ◦ Basic statistics of differentially expressed genes Results so far Matthew Price ◦ Script for listing the top 100 expressed genes ◦ Script for determining GC-content, transcript & intron length ◦ Script for getting correlation between each transcript property and the expression level Thijs Slijkhuis ◦ Created a shell script that: Downloads the source files Converts SRA into FASTQ files Performs bowtie2-build Performs tophat Performs cufflinks ◦ Programmed a script that sorts cuffdiff output on p-value (significance in differential expression), extracts gene names from it Issues/Challenges Co-expressed Genes Modules ◦ WGCNA package not usable in our case ◦ Use cummeRbund package to get Heatmaps GO enrichment analysis ◦ Not many genes are annotated in the GO database. ◦ Gene id of the differentially expressed genes are not compatible with the NCBI database. Transcript sequences ◦ Not all expressed transcripts in the .gtf file can be matched to their corresponding sequence in the fasta file. Thank you for your attention!