Pop's Pipes Gene Expression Analysis Tool
Pop's pipes: poplar gene expression data analysis pipelines

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Introduction to Pop's Pipes: Poplar Gene Expression Pipelines

1. DEG pipeline

DEG 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 Pipeline

Protein domain enrichment analysis pipeline is designed to identify the enriched protein domains from DEG list in the background of genome.


3. GO pipeline

Gene 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 pipeline

Pathway 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 pipeline

GO-tree pipeline is designed to construct GO hierarchical tree using a group of GO terms and their enrichment p-values generated by GO pipeline.


6. Citation

Li, X, C. Gunasekara, Y. Guo, H. Zhang, L. Lei, S. Tunlaya-Anukit , V. Busov, V. Chiang, and H. Wei. 2014. Pop’s Pipes : poplar gene expression data analysis pipelines (http://sys.bio.mtu.edu/index.php ). Tree Genetics & Genome.

Have comments or report problems, please send email to hairong@mtu.edu or cjgunase@mtu.edu ! !

Gene Expression Analysis Tool





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