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Module 2: Connect TFs to Target Genes

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Yaoxiang Li edited this page Feb 7, 2026 · 15 revisions

Overview (Module 2)

Input:

  • A combined multi-omic data object containing normalized signal matrices, binary flag matrices, and annotations from Module 1
  • Optional: A 3D chromatin interaction loop file (example) module_2

Process:

  1. Link TF(s) with target genes using the link_tf_targets() function.

    1.1. Link TF binding sites (TFBS; from Module 1) to candidate target genes using GeneHancer enhancer–gene mappings (default), user-defined genomic distance constraints (e.g., within 30 kb of the TSS), or a user-supplied 3D chromatin interaction loop file. These options are specified in the *.yaml configuration file.

    1.2. Generate a binary, condition-specific TF->TFBS->target link status matrix. A link is flagged as 1 in a given condition ONLY if (i) both the TF and the target gene pass the expression cutoff specified in the *.yaml file, and (ii) the corresponding footprint and peak are both flagged as bound, and (iii) both footprint score and peak signal exceed their respective cutoffs specified in the *.yaml file .

    1.3. For TF->target links with link_status(condition) = 1 in at least one condition, compute pairwise Pearson correlations between TF expression and candidate target gene expression across all matched conditions. For TFBS->target links, subsequently compute Spearman (rank-based) followed by Pearson (linear) correlations between normalized footprint scores (or peak signals if footprint scores are not available) and candidate target gene expression across all matched conditions. After each correlation step, links that fail to meet the cutoffs specified in the *.yaml configuration file are removed.

  2. Generate and output per-condition link summary matrices ready for downstream GRN analysis using the extract_link_info_by_condition() function.

Output:

  • A TF->TFBS->target link overview table containing condition-specific link status flags and correlation statistics, a summary table of active link counts per TF per condition and a corresponding PDF containing summary statistic plots comparing total active links per condition and active link counts per TF per condition.
  • A directory containing per-condition link matrices containing TF and target expression, footprint (if available) and peak signals/binding status, formatted for direct GRN visualization or differential GRN analysis.

Quick start (Module 2)

# Link and correlate TF and TFBS with potential target genes
links <- link_tf_targets(data_object) 

# Output per-condition summary of TF->TFBS->Target links
extract_link_info_by_condition(data_object, links, qc = TRUE)

Key options (YAML)

  • priors_mode: genehancer | tss_window | loop_file
  • tss_window_bp: 30000
  • loop_file: path to 3D loop file (if provided)

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