A simple registration is required to use this tool. Once registered, you can login anytime with your selected email address and password.

Query Input:

Input form image
  1. Select Query Type:
    • Search for genetic functionalogs for a gene: Returns the relevant section of the genetic (siRNA+miRNA) cluster (Supplemental Figure 2A) for display of cluster-based relationships together with rank-ordered nearest neighbors of the query gene based on the selected distance or correlation metric.

    • Search for chemical functionalogs for a gene: Returns a rank-ordered list of nearest neighbor natural product fractions based on the selected distance or correlation metric.

    • Compare a pair of genes for their functional similarity: Returns the user-selected distance or correlation between a gene pair.
      • Input: Requires one gene pair separated by a comma and/or whitespace.
        (e.g. “AKT1, AKT2”)

  2. Select a distance or correlation metric from the indicated drop-down menu:
    • Euclidean distance sum (default)
    • Mahalanobis distance sum
    • Euclidean distance rank sum
    • Pearson correlation.

  3. Select a false discovery rate filter (FDR cutoff) from the drop-down menu:
    • TOP 100 (default): 100 functionalogs with the lowest p value.
    • GET ALL: No filter (only available if APC is matched).
    • FDR<0.1
    • FDR<0.2
    • FDR<0.3
    • FDR<0.4
    • FDR<0.5

  4. Select checkbox to return functionalogs that match the queried gene's cluster number determined by Affinity Propagation Clustering (APC) algorithm. APC is only available for metrics:
    • Euclidean distance sum (default)
    • Pearson correlation

  5. Input the gene or miRNA symbol of interest.
    • Only 1 symbol for functionalog search and 2 for comparison.
    • Input requires an appropriate HUGO gene symbol (case insensitive).
    • A list of currently queryable gene symbols is .

Output Description:

Results table example
  1. Associated Subcluster: Heatmap of the subcluster associated with gene of interest. Derived from clustering the complete kinome+miRNA dataset.
  2. Symbol: Gene symbol or name of the natural product.
  3. Metric: Sum of triplicate measures (Dist1, Dist2, Dist3).
    • Distsum: Euclidean distance sum
    • Mahalanobis: Mahalanobis distance sum
    • Ranksum: Euclidean distance rank sum
    • Pearson: Pearson correlation
  4. P-value & FDR: Obtained from permuted dataset. FDR value is displayed only when it is less than 0.5. See Supplemental Methods for details.
  5. APC: Cluster number is determined by the apcluster R package using the specified distance metric.
  6. BNIP3L, NDRG1, ALDOC, LOXL2, BNIP3, ACSL5: LOG2 transformed normalized gene expression values for each of the 6 reporter genes.

Output Management

Output managemet table
  1. Query Parameters: Displays search parameters for the current query results.
  2. Output Options
    • Distance Table: Download CSV file containing the distance table (Symbol, Metric, Dist1-3, P value, FDR, APC).
      Queried gene data is NOT included.
    • Expression Table: Download CSV file containing Log2 expression values of functionalogs.
      Queried gene expression is included.
    • Cluster Expression: Hierarchically cluster the Log2 expression results from the current query. Get PDF file.
  3. Display Options
    • Expression Heat Map: Collapse gene expression numeric values for quick comparisons.
    • Heatmap Data Box: Display text box in lower left corner to display heatmap cell data.
    • Persistent Row: Always display queried gene row as you scroll down.
    • Associated Subcluster: Display all images of subclusters associated with the gene of interest.