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ROBUST-Web only runs on screens bigger than 768px in width.




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ROBUST-Web only runs on screens bigger than 768px in width.



ROBUST

ROBUST performs disease module mining (DMM) via the enumeration of prize collecting Steiner Trees (PCST). Given a graph with non-negative edge costs and node prizes, we try to find a subgraph that connets the given nodes to the nodes with the highest prizes, and including the edges with the highest edge weights. The node prizes are initialized using seeds provided by the user, and are updated with the progression of the algorithm.


In mathematical terms: Given a graph \(\mathbf{G=(V,E,c,\boldsymbol{\pi})}\), with non-negative edge costs \(\mathbf{c}\) and node prizes \(\boldsymbol{\pi}\), the PCST-problem tries to find a tree \(\mathbf{T=(V_T, E_T) \boldsymbol{\subseteq} G}\), minimizing \(\mathbf{\sum_{uv \boldsymbol{\in} E_T}c(uv)+\sum_{u \boldsymbol{\in} V\setminus V_T}\boldsymbol{\pi}(u)}\).


In ROBUST-Web, we provide the option of running ROBUST using custom or in-built study bias data. The bias-aware edge weights have been calculated using the following equation:

\( \mathbf{ c(uv)=\boldsymbol{\gamma}\cdot\max\{f(u),f(v)\}+(1-\boldsymbol{\gamma})\cdot\frac{\sum_{u^\boldsymbol{\prime} v^\boldsymbol{\prime} \boldsymbol{\in} E}\max\{f(u^\prime),f(v^\prime)\}}{|E|} } \),
where \(\mathbf{f(u)}\) is the degree of over-representation of protein \(\mathbf{u}\) in PPI networks
and, \(\boldsymbol{\gamma}\) is the extent to which study bias data has been leveraged in the calculation of edge weights.


Alternatively, when no study bias data is selected, the default version of ROBUST with uniform edge costs is implemented, where \(\mathbf{c(uv)=1}\) for all edges \(\mathbf{uv}\).


Parameters

Input specifications and error codes

  1. seeds
    • Input specifications:
      File type allowed Data format allowed
      • Any text file type (including, but not limited to: .tsv, .csv and .txt).
      • Can also be uploaded manually.
      • space-separated
      • newline-separated

    • Error codes:
      Use case Error message
      No seeds uploaded.
      ‘Seeds cannot be empty’


  2. network
    • Input specifications:
      File type allowed Data format allowed
      • Select from in-built: BioGRID, APID and STRING.
      • Upload .graphml file
      • Any text file type (including, but not limited to: .tsv, .csv and .txt)
      • Can also be uploaded manually.
        A space-separated edgelist with at least 2 columns, and at least one element in the first two columns (excluding the column header).

    • Error codes:
      Use case Error message
      If ‘Upload custom network’ option selected, but no network uploaded.
      ‘Custom network has to be uploaded!’
      If columns with zero elements in the first two columns (excluding header), is uploaded.
      ‘Custom network has to be uploaded!’
      If only one column uploaded.
      ‘Custom network with less than two columns uploaded. Please add two columns.’
      If 3 or more columns uploaded.
      No error message: The first two columns retained.


  3. study bias data
    • Input specifications:
      File type allowed Data format allowed
      • Select from in-built study bias datasets: Bait usage or Study attention. Note that the default option No just runs ROBUST with uniform edge weights (i.e., not making use of any study bias data).
      • Upload file (including, but not limited to: .tsv, .csv and .txt).
      • Can also be uploaded manually.
        At least 2 space-separated columns, and at least one element in the first two columns. The first columns should contain the node name; the second column should contain study bias information pertinent with the node. Note that the second column elements must be of type integer (\(\mathbf{Z}\)).

    • Error codes:
      Use case Error message
      If ‘CUSTOM’ option selected in ‘Normalize by’ parameter, but no data uploaded.
      ‘Custom study bias data has to be uploaded!’
      If columns with zero elements in the first two columns (excluding header), is uploaded.
      ‘Custom study bias data has to be uploaded!’
      If only one column uploaded.
      ‘Custom study bias data with less than two columns uploaded. Please add two columns.’
      If 3 or more columns uploaded.
      No error message: The first two columns retained.