PY1H reproducibility

Predicting possible TF-TF interactions based on homology.

Possible TF-TF heterodimers were derived from LitBM. Check this notebook

Bioinformatics analysis of TF-prey sequencing data

Input Files

1. barcodes_fw.fasta and barcodes_rv.fasta: Barcode sequences to perform demultiplexing of Fastq files
2. Fastq Files are deposited at link
3. Het array with Ensembl Gene IDs.xlsx

Scripts

1. trimming.sh: Demultiplexing and trimming of Fastq files.
2. get_enst_biomaRt.R: Get all transcript sequences for expected TFs in PY1H experiment.
3. fromTxttoFasta.py: Converts to fasta file.
4. BowtieMaping.sh: Index library, align FASTQ files, and generates bam files.
5. Get_Significant_Pairs.R: Identify significant alignments and TF-TF pairs.

Output Files

1. PGADT7_AD2U_results.txt

Manual revision of detected TF-TF-cytokine interactions

Input Files

1. PGADT7_AD2U_results.txt

Output Files

1. Final events list 6Feb23.xlsx: 437 TF-TF-cytokine interactions experimentally identified with PY1H (180 cooperative, 257 antagonism).

Obtaining ChIP-seq data from GTRD

Input Files

1. Final events list 6Feb23.xlsx: 437 TF-TF-cytokine interactions experimentally identified with PY1H (180 cooperative, 257 antagonism).

Scripts

1. download_gtrd.py: Download MACS2 ChIP peaks from GTRD and metadata information.
2. script_CHIPSEQ.py: Get information on peaks between our TFs of interest and the respective cytokine promoters.

Output Files

1. MACS2_Peaks_TFs_final_16_feb.xlsx

Identification of binding sites of TF-pairs in cytokine promoters

Input Files

1. Final events list 6Feb23.xlsx: 437 TF-TF pairs experimentally identified with PY1H (180 cooperative, 257 antagonism)
2. promoters.fasta: Fasta file of cytokine promoters coded explained in the previous Excel file.

Scripts

1. PWMs were downloaded from CISBP 2.0 database including pwms_all_motifs directory and TF_information.txt file.
2. TFPM_motifs_identification.R: Script to calculate significant TF motifs identified in cytokine promoters.
3. Promoter_Analysis_merged.Rmd: Script to merge overlapping TF motifs that were previously identified.

Output Files

1. motifs_results_merged_motifs.xlsx
2. DF_all_motifs.xlsx

Network Randomization Analysis (Promoters)

Input Files

1. Final events list 6Feb23.xlsx: 437 TF-TF pairs experimentally identified with PY1H (180 cooperative, 257 antagonism)
2. DF_all_motifs.xlsx: Table containing motifs information for each TF-TF-cytokine interaction.

Scripts

Promoter_Randomization.Rmd: Script to perform randomization and reproduce Supplementary Figure 6 C, D, E

Output Files

Supplementary Figure 6C, 6D, 6E

Network Randomization Analysis (ChIP peaks)

Input files

1. Final events list 6Feb23.xlsx: 437 TF-TF pairs experimentally identified with PY1H (180 cooperative, 257 antagonism)
2. all_tfs_chipseq.txt: Table with TF name and Uniprot ID.
3. ChIP-seq.metadata.txt: Metadata file from GTRD database.
4. MACS2_Peaks_TFs_final_16_feb.xlsx: Peaks information for TF in pY1H

Scripts

CHIP_Randomization_antagonism.Rmd: Script to perform randomization and reproduce Figure 2G; and Supplementary Figure 6F, G

Output Files

Figure 2G; Supplementary Figure 6F, 6G

Network Randomization Analysis (EY1H and PY1H with ChIP data)

Input files

1. py1h ey1h chip-seq overlap list for Luis.xlsx: 270 TF-promoter from eY1H and 256 TF-promoter from pY1H
2. all_tfs_chipseq.txt: Table with TF name and Uniprot ID.
3. MACS2_Peaks_TFs_final_26_june.xlsx: Peaks information for TF in eY1H
4. MACS2_Peaks_TFs_final_16_feb.xlsx: Peaks information for TF in pY1H

Scripts

Reviewers_randomization.Rmd

Output Files

Figure X.

Paralog partner similarity

Input files

1. proteins.fasta: Protein sequences for TFs with Uniprot ID obtained from UNIPROT
2. uniprot.tsv: Metadata table from Uniprot
3. Array TF families.xlsx: TFs from pY1H and TF Family
4. 297 pairs coop+ant events.xlsx:

Scripts

1.Jaccard_Analysis.Rmd

Output Files

1. Paralog_analysis_output.xlsx: Jaccard score and alignment score for each pair of TF
2. Figure 3D