Integrative Inference of De Novo Cis-Regulatory Modules

A | TF-gene regulation strength matrix |

alpha | Inverse-gamma distribution hyper-parameter alpha |

A_old | TF-gene regulation strength matrix sampled from the previous... |

A_sampling | Regulation Strength Sampling Function |

base_line | Gene baseline expression |

base_line_old | Gene baseline expression sampled from the previous round. |

baseline_sampling | Gene Baseline Expression Sampling Function |

beta | Inverse-gamma distribution hyper-parameter beta |

BICORN | BICORN Algorithm Function |

Binding_genes | Genes in the prior binding network |

Binding_matrix | Prior TF-gene binding network |

Binding_TFs | TFs in the prior binding network |

C | TF-gene binding network |

C_old | TF-gene binding network sampled from the previous round |

C_prior | Prior TF-gene binding network |

C_sampling_cluster | cis-Regulatory Module Sampling Function |

data_integration | Data Initialization for BICORN |

Exp_data | Gene expression data |

Exp_genes | Genes in the expression data |

sigma_A | Regulation strength variance |

sigma_baseline | Variance of baseline gene expression. |

sigma_noise | Variance of gene expression fitting residuals. |

sigmanoise_sampling | Fitting Residule Variance Sampling Function |

sigma_X | Transcription factor activity variance |

X | Transcription factr activity matrix |

X_old | Transcription factr activity matrix sampled from the previous... |

X_sampling | Transcription Factor Activity Sampling Function |

Y | Gene expression data used for module inference |

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