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TimeTP manual / TimeTP-web manual

Running TimeTP

  • Make a GRN and PIN file for your species of interest (Provided for homo sapiens).
  • Make a group file, a probe-gene name file in the directory where gene expression files exist.
  • Make your own configuration file in TimeTP directory.
  • Run TimeTP by typing './TimeTP [configuration_file_name]'.

    • Making a configuration file

  • A configuration file should be a tab-delimited, two-columned file including the contents below.
  • Sample file is included in the package.

    • type 'RNA-seq' or 'Microarray'
    readType Only for RNA-seq data. 'single-read' OR 'paired-end'
    dataDir Path to the directory that includes your files (CEL or raw count).
    outDir Path to the output directory that results will be saved.
    species KEGG organism code with three characters. It can be found at http://www.kegg.jp/kegg/catalog/org_list.html
    downloadFiles yes or no to download relevant files from KEGG, including a KEGG gene name file, a KEGG pathway list file and XML files for each pathway.
    If you say 'no', you should provide the file paths in 'KEGGGeneFilePath', 'KEGGPathFilePath' and 'xmlFilePath'.
    If you say 'yes', the files will be downloaded in the /.../TimeTP/[species] folder.
    KEGGGeneFilePath (Write only when you wrote 'no' in 8). Path to KEGG-Gene symbol file. You can download it as http://rest.kegg.jp/list/[KEGG_organism_code]
    KEGGPathFilePath (Write only when you wrote 'no' in 8). Path to KEGG pathway list file. You can download it as http://rest.kegg.jp/list/pathway/[KEGG_organism_code]
    xmlFilePath (Write only when you wrote 'no' in 8). Path to a directory consisting of XML files from each KEGG pathway.
    single '0' for Control-Treatment samples and '1' for single time-series samples.
    countFile Only for RNA-seq data. Name of the raw read count input file. Please refer to 'Expression files' section.
    groupFile Name of the group file. See the 'Group file and gene conversion file' section.
    geneConvFile Name of the gene conversion file. See the 'Group file and gene conversion file' section.
    numTP The number of time points.
    threshold Threshold for P-value (Default : 0.05)
    maxDelay Maximum delay of expression propagation (Default : 1).
    1 implies TimeTP allows expression propagation across one time point or less. It depends on whether time interval between time-series samples are short or long.
    removeT0 '1' for removing DEGs found in the first time point and '0' for not removing them. (Default : 0 for single time-series, 1 for control-treatment)
    FDR '1' for using FDR corrected P-value for DEG selection and '0' for not using it.
    (Default : 1)
    k The maximum number of TFs to find by influence maximization algorithm.
    (Default: 20)

    Group file and gene conversion file

    Group file Group file consists of two columns (tab-delimited).
    • First column : Group number
      • Single time-series samples
        • Samples for the first time point : 0
        Samples for the second time point : 1
        ...
        Samples for the Nth time point : N-1
      • Control-treatment time-series samples
        • Control samples for the first time point : 0
        Control samples for the second time point : 1
        ...
        Control samples for the Nth time point : N-1
        Treatment samples for the first time point : N
        ...
        Treatment samples for the Nth time point : 2N-1
    • Second column : Sample names
      • Microarray
        • Same as CEL file names.
      • RNA-seq
        • Same as column headers of countFile.
    Gene conversion file Gene conversion file consists of two columns (tab-delimited).
    • First column : Probe name
    • Second column : Gene symbol
      • (Entrez ID or Official gene symbol)
      If row headers in countFile are already gene symbols, geneConvFile can be specified as 'NA'.

    Expression files

    Microarray CEL files.
    File names of the CEL files should be in the second column of groupFile.
    RNA-seq Raw read count files, comma-delimited with column and row headers.
    Column headers should match the second column of groupFile. The number of column headers should be same as the number of samples. Row headers should match the first column of geneConvFile OR should be gene symbols.

    Result files

    DEG_result.T*.txt
    DEG_profile.txt    		 DEG_results files are created from DEG analysis by Limma or DESeq2 for each time point. The result is summarized into DEG_profile using p-value threshold that user specified.
    webpage/
    network_overview.html    		 TF-Pathway map in time clock described in the TimeTP paper. Paths from TFs to perturbed subpathways are shown.
    webpage/
    index.html    		 A list of perturbed subpathways and their p-values, link to diagram for each subpathway.

    contact

    keialk@snu.ac.kr Bio & Health Lab., Seoul National University