Identification of potential riboswitch elements in Homo Sapiens mRNA 5'UTR sequences using Positive-Unlabeled machine learning

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William S. Raymond¹, Jacob DeRoo¹, Brian Munsky^1,2

^{1 School of Biomedical Engineering, Colorado State University Fort Collins, CO 80523, USA}

^{2 Chemical and Biological Engineering, Colorado State University Fort Collins, CO 80523, USA}

This repository contains all the final data files used for the analysis in the above manuscript.

├─  algnment_matrices/ - alignment matrices for the ranking metrics in the paper
│		├─ levdist_array_1533.npy 
│		├─ utr_hits_ldiff_mse_1533.npy
│		├─ utr_hits_mse_1533.npy
├─  analysis_files/ - alignment matrices for the ranking metrics in the paper
│		├─ importances.npy
├─  data_files/ - raw and processed data files used to make the feature sets
│		├─ CCDS_nucleotide.current_11.28.2021.fa 
│		├─ riboswitch_RNAcentral_8.19.21.json 
│		├─ rs_dot.json
│		├─ RSid_to_ligand.json 
│		├─ 5primeUTR_final_db_3.csv 
│		├─ RS_final_with_euk2.csv 
│		├─ RS_id_to_ligand.csv 
│		├─ species_in_RS_set.txt
│		├─ 5UTRaspic.Hum 
├─  elkanoto_models/ - PUlearn models
│		├─ EKmodel_witheld_w_struct_features_9_26_%%LIGAND%%_%%LIGAND%%.joblib
│		├─ load_ensemble.py
│		├─ utr_proba_norm.npy
├─  ensemble_predictions/ - predictions from the ensemble classifier
│		├─ all_utr_predictions.npy
│		├─ final_set_436.json
│		├─ final_set_1533.json
│		├─ utr_dot_hits_1533.json
│		├─ utr_proba_norm.npy
│		├─ utr_proba_1533.npy
├─  feature_npy_files/ - extracted feature data arrays
│		├─ X_RS_full.npy
│		├─ X_UTR.npy
│		├─ X_SYN.npy
│		├─ X_EXONs.npy
│		├─ X_RAND.npy
│		├─ ids_UTR.npy
│		├─ ids_RS.npy
├─  Figures/  ─  figure files for the paper
├─  GO/ ─  GO analysis output files 
│		├─ component_436.txt
│		├─ component_1533.txt
│		├─ function_436.txt
│		├─ function_1533.txt
│		├─ process_436.txt
│		├─ process_1533.txt
│		├─ gene_list_436.txt
│		├─ gene_list_1533.txt

Contact info: [email protected]