The Landscape of SETBP1 Gene Expression and Transcription Factor Activity across Human Tissues

New publication DOI included from PLOS ONE. Published January 2, 2024.

Docker image and updated clustering addition release

The code and results in this repository accompany the "The landscape of SETBP1 gene expression and transcription factor activity across human tissues" manuscript.

The repository includes the following:
/data/: this directory contains the inputs used for SETBP1 target gene set construction and the final converted output file of human HGNC symbols with a description for each gene.

/src/:

Tissue_Expression/: includes code to generate SETBP1 target gene set combined from multiple resources including TRRUST, SIGNOR, MSIGDB, and literature references. In addition, we analyze and visualize the expression and perform pathway enrichment analyses on SETBP1 and its known targets.
tf_activity/: includes code to analyze TF activity of SETBP1 and its known targets across 31 human GTEx tissues and visualize the outputs.
/results/:

SETBP1_Expression/: directory containing all TPM files for each of the 31 tissues, a plots subdirectory with outputs from our analyses, and a versions_packages subdirectory. In addition, the aggregated_tissues_tpm_median.csv and setbp1_target_cor_clust.csv files are included here.
array_inputs/: contains the "GTEx_exp_files_array.txt" of inputs for running array jobs using the multivariate linear model to infer TF activity.
tf_activity/: contains the full list of activity scores for all 758 TFs across human GTEx tissues
setbp1_targets.csv: the file containing the setbp1_targets.csv used as input for human gene set construction. Originally preprinted here: https://www.biorxiv.org/content/10.1101/2023.07.31.551338v1 and published in PLOS ONE here: https://doi.org/10.1371/journal.pone.0296328
In addition, all code for our Shiny application can be found at: https://github.com/lasseignelab/gtex_tf_activity

The landscape of SETBP1 gene expression and transcription factor activity across human tissues

New docker image and updated clustering addition release

The code and results in this repository accompany the "The landscape of SETBP1 gene expression and transcription factor activity across human tissues" manuscript.

The repository includes the following:
/data/: this directory contains the inputs used for SETBP1 target gene set construction and the final converted output file of human HGNC symbols with a description for each gene.

/src/:

Tissue_Expression/: includes code to generate SETBP1 target gene set combined from multiple resources including TRRUST, SIGNOR, MSIGDB, and literature references. In addition, we analyze and visualize the expression and perform pathway enrichment analyses on SETBP1 and its known targets.
tf_activity/: includes code to analyze TF activity of SETBP1 and its known targets across 31 human GTEx tissues and visualize the outputs.
/results/:

SETBP1_Expression/: directory containing all TPM files for each of the 31 tissues, a plots subdirectory with outputs from our analyses, and a versions_packages subdirectory. In addition, the aggregated_tissues_tpm_median.csv and setbp1_target_cor_clust.csv files are included here.
array_inputs/: contains the "GTEx_exp_files_array.txt" of inputs for running array jobs using the multivariate linear model to infer TF activity.
tf_activity/: contains the full list of activity scores for all 758 TFs across human GTEx tissues
setbp1_targets.csv: the file containing the setbp1_targets.csv used as input for human gene set construction. Originally published here: https://www.biorxiv.org/content/10.1101/2023.07.31.551338v1
In addition, all code for our Shiny application can be found at: https://github.com/lasseignelab/gtex_tf_activity

The Landscape of SETBP1 Gene Expression and Transcription Factor Activity across Human Tissues

Citation addition release

The code and results in this repository accompany the "The landscape of SETBP1 gene expression and transcription factor activity across human tissues" manuscript.

The repository includes the following:
/data/: this directory contains the inputs used for SETBP1 target gene set construction and the final converted output file of human HGNC symbols with a description for each gene.

/src/:

• Tissue_Expression/: includes code to generate SETBP1 target gene set combined from multiple resources including TRRUST, SIGNOR, MSIGDB, and literature references. In addition, we analyze and visualize the expression and perform pathway enrichment analyses on SETBP1 and its known targets.
• tf_activity/: includes code to analyze TF activity of SETBP1 and its known targets across 31 human GTEx tissues and visualize the outputs.

/results/:

• SETBP1_Expression/: directory containing all TPM files for each of the 31 tissues, a plots subdirectory with outputs from our analyses, and a versions_packages subdirectory. In addition, the aggregated_tissues_tpm_median.csv and setbp1_target_cor_clust.csv files are included here.
• array_inputs/: contains the "GTEx_exp_files_array.txt" of inputs for running array jobs using the multivariate linear model to infer TF activity.
• tf_activity/: contains the full list of activity scores for all 758 TFs across human GTEx tissues
• setbp1_targets.csv: the file containing the setbp1_targets.csv used as input for human gene set construction. Originally published here: https://www.biorxiv.org/content/10.1101/2023.07.31.551338v1

In addition, all code for our Shiny application can be found at: https://github.com/lasseignelab/gtex_tf_activity

The landscape of SETBP1 gene expression and transcription factor activity across human tissues

Repo, Docker, Shiny Application, and Data DOI release

The code and results in this repository accompany the "The landscape of SETBP1 gene expression and transcription factor activity across human tissues" manuscript.

The repository includes the following:
/data/: this directory contains the inputs used for SETBP1 target gene set construction and the final converted output file of human HGNC symbols with a description for each gene.

/src/:

• Tissue_Expression/: includes code to generate SETBP1 target gene set combined from multiple resources including TRRUST, SIGNOR, MSIGDB, and literature references. In addition, we analyze and visualize the expression and perform pathway enrichment analyses on SETBP1 and its known targets.
• tf_activity/: includes code to analyze TF activity of SETBP1 and its known targets across 31 human GTEx tissues and visualize the outputs.

/results/:

• SETBP1_Expression/: directory containing all TPM files for each of the 31 tissues, a plots subdirectory with outputs from our analyses, and a versions_packages subdirectory. In addition, the aggregated_tissues_tpm_median.csv and setbp1_target_cor_clust.csv files are included here.

• array_inputs/: contains the "GTEx_exp_files_array.txt" of inputs for running array jobs using the multivariate linear model to infer TF activity.

• tf_activity/: contains the full list of activity scores for all 758 TFs across human GTEx tissues

• setbp1_targets.csv: the file containing the setbp1_targets.csv used as input for human gene set construction. Originally published here: https://www.biorxiv.org/content/10.1101/2023.07.31.551338v1

In addition, all code for our Shiny application can be found at: https://github.com/lasseignelab/gtex_tf_activity

The landscape of SETBP1 gene expression and transcription factor activity across human tissues

Initial Release

The code and results in this repository accompany the "The landscape of SETBP1 gene expression and transcription factor activity across human tissues" manuscript.

The repository includes the following:
/data/: this directory contains the inputs used for SETBP1 target gene set construction and the final converted output file of human HGNC symbols with a description for each gene.

/src/:

• Tissue_Expression/: includes code to generate SETBP1 target gene set combined from multiple resources including TRRUST, SIGNOR, MSIGDB, and literature references. In addition, we analyze and visualize the expression and perform pathway enrichment analyses on SETBP1 and its known targets.
• tf_activity/: includes code to analyze TF activity of SETBP1 and its known targets across 31 human GTEx tissues and visualize the outputs.

/results/:

• SETBP1_Expression/: directory containing all TPM files for each of the 31 tissues, a plots subdirectory with outputs from our analyses, and a versions_packages subdirectory. In addition, the aggregated_tissues_tpm_median.csv and setbp1_target_cor_clust.csv files are included here.

• array_inputs/: contains the "GTEx_exp_files_array.txt" of inputs for running array jobs using the multivariate linear model to infer TF activity.

• tf_activity/: contains the full list of activity scores for all 758 TFs across human GTEx tissues

• setbp1_targets.csv: the file containing the setbp1_targets.csv used as input for human gene set construction. Originally published here: https://www.biorxiv.org/content/10.1101/2023.07.31.551338v1

In addition, all code for our Shiny application can be found at: https://github.com/lasseignelab/gtex_tf_activity