Log-linear Graphical Model

: inferring probabilistic conditional independency from combinatorial regulation of transcription factors

To run LLGM,
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Transcription factors (TFs) regulate gene expressions by intricate combinatorial interactions. Computational modeling to infer the interactions is essential to understand the nature of transcriptional regulation. Log-linear Graphical Model (LLGM) deals with spurious TF interactions that may lead to deceptive inferences. Given a discrete (0 or 1) input data matrix of TF-DNA binding instances, the LLGM estimates the probabilistic conditional independency for detecting the spuriousness, which is known as "Simpson's Paradox".


The format of the input matrix file:
  • Input data is a n x m matrix, where n is the number of promoters (genes) and m column is the number of TFs.
  • The input file has to include a line "#ITEM: TF1 TF2 TF3", where "TF1" is an item.
  • The absence or presence of one item is denoted by "1 0" or "0 1".
  • Each line has to be TAB deliminated; e.g. 'Promo_A[tab]0[tab]1[tab]1[tab]0[tab]1[tab]0'.
  • 'Promo_A[tab]0[tab]1[tab]1[tab]0[tab]1[tab]0' means that the "Promo_A" includes
    • "0 1" (=presence) of TF1
    • "1 0" (=absence) of TF2
    • "1 0" (=absence) of TF3.
  • [see an example input data]

  • Two thresholds are required for running:
    1. p-value cutoff for the test of deviance of a current RM (reduced model) from the FM (full model)
    2. p-value cutoff for the test of deviance of a current RM (reduced model) from the previous RM

  • In this web-version, the matrix size n and m is restricted to 50≤ n ≤2000 and 2≤ m ≤10.
  • You can request it for an extension by contacting us.

  • Reference
    1. Lauritzen, S.L., "Graphical Models", Oxford University Press, 1996
    2. Christensen, R., "Log-Linear Models and Logistic Regression", Springer-Verlag, 1997
    3. Park SJ, Umemoto T, Saito-Adachi M, Shiratsuchi Y, Yamato M, Nakai K, "Computational Promoter Modeling Identifies the Modes of Transcriptional Regulation in Hematopoietic Stem Cells", PLoS ONE 9(4): e93853, 2014