1. BIF Group Project
Group (A)rabidopsis: David Nieuwenhuijse Matthew Price Qianqian Zhang Thijs Slijkhuis
Species: C. Elegans
Project:
Advanced (+Basic)

2. Progress Report

3. 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

4. Results so far David Nieuwenhuijse Qianqian Zhang
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

5. Results so far Matthew Price Thijs Slijkhuis
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

6. Issues/Challenges Co-expressed Genes Modules GO enrichment analysis
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.

7. Thank you for your attention!