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Introduction to Pop's Pipes: Poplar Gene Expression Pipelines |
1. DEG pipelineDEG pipeline is designed to identify differentially expressed genes (DEGs) from any comparisons of genes expressed in two tissues, two timepoints or two experiment conditions.
2. Domain PipelineProtein domain enrichment analysis pipeline is designed to identify the enriched protein domains from DEG list in the background of genome.
3. GO pipelineGene ontology (GO)-Term enrichment analysis pipeline is designed to identify the enriched gene ontology terms for a list of DEGs in the background of genome. Those gene ontology terms include: A. Biological process, which refers to a biological process to which the gene or gene product contributes. B. Molecular Function, which defined as the biochemical activity of a gene product. C. Cellular component, which refers to the place in the cell where a gene product functions.
4. Pathway pipelinePathway pipeline is designed to identify differentially expressed pathways (sets) in DEG list compared to genome background using SAM-GS (Dinu et al, 2007, BMC Bioinformatics 2007, 8:242)5. GO-tree pipelineGO-tree pipeline is designed to construct GO hierarchical tree using a group of GO terms and their enrichment p-values generated by GO pipeline.Have comments or report problems, please send email to hairong@mtu.edu or cjgunase@mtu.edu ! feedback! |
Copyright 2012/2013 MTU School of Forest |
Designed by Yufeng Guo, Xiang Li and Chathura Gunasekara
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