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

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Pop's pipes:

Identification of Differentially Expressed Poplar Genes(DEGs)

1. Select data platform type:

1.1 Select Method for RNA-seq Normalization and Analysis (RNA-seq only)

2. Upload the gene expression data file: ( Check microarray input file format ) ( Check RNA-seq input file format )

Note that:
(1) The input .txt file name should not contain any white spaces
(2) Control column names must begin with C, whereas treatment column names begin with T
(3) For each time point/comparison, control data are listed at left, and treatment data at right.
(4) (Recommended) Please save the data file in tab delimited text file format from Microsoft Excel from a Windows Computer [help?]

3. Enter the NUMBER of all time points or comparisons (e.g. treatments vs control):

4. Microarray Data (only): Precentage for trimming (lowly expressed genes) (e.g. 0.1`- 10%; 0 - do not trim):

5. High Throughput Sequencing Data (only): Enter the minimum values allowed:(Set values smaller than this to this value. Default minimum value is 1):

5. Enter cut-off corrected p-value(FDR) for selecting DEGs (e.g. 0.05):

6. Do you want to run the following analyses upon running DEG analysis? (you are encouraged to run them at one time. However, you can always examine the DEG output first and then come back to load the DEG output and run the following analyses at a later time)

Metabolic Pathway Enrichment Analysis (Gene Set Enrichment Analysis)

Protein Domain Enrichment Analysis

Gene Ontology (GO) Enrichment Analysis

Gene Expression Analysis Tool

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