FANTOMUS: Molecular Phenotypes of Diverse Human Skeletal Muscles

FANTOMUS: gene expression and protein abundance profiles of diverse human skeletal muscles This repository provides transcribed regulatory element (TRE) activity estimates, protein abundance, transcription factor motif activities, and allele-specific single-nucleotide variants. Contents Zip-archives FANTOMUS_MARADONER.zip This archive contains the data used for the Motif Activity Response Analysis with MARAdoner, including transcribed regulatory element (TRE) activity estimates (CAGE_clusters_expression_logCPM_H14.tsv), TRE-level sum-occupancy scores for 585 HOCOMOCO v14 representative motifs (TF_clusters_occupancy_250u_10d_H14.tsv), total expression levels of the corresponding transcription factors (TF_clusters_expression_logCPM_H14.tsv), and the necessary sample-level metadata (Sample_groups_H14.tsv). Additionally, the archive contains 4 folders with the full MARADONER output, including the estimated model parameters (params) and motif activities (activities), the results of the statistical tests for mean and differential activity (tests), as well as the Bayesian beliefs computed by MARADONER GRN prediction (belief). File formats: plain text and hdf5. Please refer to MARADONER documentation (https://github.com/autosome-ru/MARADONER) for technical details. FANTOMUS_MIXALIME.zip This archive contains tsv files with the single-nucleotide variants detected from CAGE-Seq data and the allelic imbalance estimates obtained with MIXALIME. Each file corresponds to one of the 75 skeletal muscles of FANTOMUS. Please refer to MIXALIME documentation (https://github.com/autosome-ru/mixalime) for technical details. bedGraph_full.zip This archive contains 222x2 (222 samples, + and - strands, separately) bedGraph profiles counting 5' ends of all uniquely mapped CAGE-Seq reads. bedGraph_softG.zip This archive contains 222x2 (222 samples, + and - strands, separately) bedGraph profiles counting 5' ends of 'softclip-G' uniquely mapped CAGE-Seq reads, likely reflecting high-confidence transcription start sites. Individual files Gene_level_counts.tsv This tsv file contains the total CAGE-Seq read counts for 18329 genes across 222 FANTOMUS samples of 75 skeletal muscles. Protein_log_intensities.tsv This tsv file contains batch-corrected and normalized log2-intensities for 1804 protein groups encompassing 1895 proteins detected in 60 FANTOMUS samples of 22 skeletal muscles using tandem mass spectrometry. TRE_level_counts_before_correction.tsv This tsv file contains raw CAGE-Seq read counts for the 37001 TREs detected in 222 FANTOMUS samples of 75 skeletal muscles. TRE_level_counts.tsv This tsv file contains batch-corrected TRE-level read counts used in FANTOMUS. EXTRA Permissive_TRE_annotation.tsv This tsv file contains the basic annotation of the permissive FANTOMUS superset: 102434 TREs passing CPM > 0.5 in 3 or more samples. Permissive_TRE_level_counts_uncorrected.tsv This tsv file contains the raw CAGE-Seq read counts for the 102434 TREs included in the permissive superset. Permissive_TRE_level_counts.tsv This tsv file contains the batch-corrected TRE-level read counts included in the permissive superset.