TissueCoCoPUTs V1.3 10_07_2020

Codon, codon pair and dinucleotide calculation performed on GenBank Release 238.0 and RefSeq Release 99.
Human tissue-specific codon, codon pair and dinucleotide usage were calculated from Homo sapiens assembly 
GCF_000001405.39 and tissue-specific gene expression data from the Genotype-Tissue Expression Portal 
(GTEx Release V8) (https://www.gtexportal.org/)

All data files are tab delimited (.tsv)

Description of files:

genbank_Bicod.tsv			Bicodon usage per species derived from GenBank files
genbank_CDS.tsv				Codon usage per CDS from all species in genbank_species.tsv
genbank_Dinuc.tsv			Dinucleotide usage per species derived from GenBank files
genbank_index.tsv			Indexing file used by interface to locate GenBank entries
genbank_JuncDinuc.tsv		Junction dinucleotide usage per species derived from GenBank files
genbank_species.tsv			Codon usage per species derived from GenBank files
Human_CDS.tsv				Codon usage per CDS from assembly GCF_000001405.39
Human_CDS_Bicod.tsv			Bicodon usage per CDS from assembly GCF_000001405.39
Human_CDS_Dinuc.tsv			Dinucleotide usage per CDS from assembly GCF_000001405.39
Human_CDS_Junc_Dinuc.tsv	Junction dinucleotide usage per CDS from assembly GCF_000001405.39
Refseq_Bicod.tsv			Bicodon usage per species derived from RefSeq assemblies
Refseq_CDS.tsv				Codon usage per CDS from all species in Refseq_species.tsv
Refseq_Dinuc.tsv			Dinucleotide usage per species derived from RefSeq assemblies
Refseq_index.tsv			Indexing file used by interface to locate RefSeq entries
Refseq_JuncDinuc.tsv		Junction dinucleotide usage per species derived from RefSeq assemblies
Refseq_species.tsv			Codon usage per species derived from RefSeq assemblies
Tissue_Bicod.tsv			Bicodon usage per tissue (human)
Tissue_Codon.tsv			Codon usage per tissue (human)
Tissue_Dinuc.tsv			Dinucleotide usage per tissue (human)
Tissue_Junc_Dinuc.tsv		Junction dinucleotide usage per tissue (human)

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CancerCoCoPUTs V1.0 	08 February 2021

Human primary tumor-specific codon, codon pair and dinucleotide usage were calculated 
from gene specific codon usage of Homo sapiens assembly GRCh38.p13 and primary tumor-specific gene expression data 
from The Cancer Genome Atlas (https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga).
RNA-seq expression files were downloaded from the National Cancer Institute’s Genomic Data Commons (GDC) 
repository (https://portal.gdc.cancer.gov/repository) accessed on 07/30/2020.

All data files are tab delimited (.tsv)

Description of files:

Cancer_Bicod.tsv				Bicodon usage per tumor / tissue (human)
Cancer_Codon.tsv				Codon usage per tumor / tissue (human)
Cancer_Dinuc.tsv				Dinucleotide usage per tumor / tissue (human)
Cancer_Junc_Dinuc.tsv			Junction dinucleotide usage per tumor / tissue (human)
paired_bicodon_usage.tsv		Paired normal / tumor bicodon data
paired_codon_usage.tsv			Paired normal / tumor codon data
paired_dinuc_usage.tsv			Paired normal / tumor dinucleotide data
paired_junc_dinuc_usage.tsv		Paired normal / tumor junction dinucleotide data
paired_cat_df.tsv				Paired normal / tumor data dictionary