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Genome Biology Abbreviations

Mehmet Tevfik DORAK

 

1KG: One thousand genome study

3C: Chromosome conformation capture

4C: Circular chromosome conformation capture

4C-seq: Circular chromosome conformation capture followed by sequencing

5C: Chromosome conformation capture carbon copy

5-hmC: 5-hydroxymethylcytosine

5-mC: 5-methylcytosine

AAS: Amino acid substitution

APBSs: High occupancy architectural protein binding sites

AR: Androgen receptor

ASM: Alternative splicing module

ASO: Antisense oligonucleotides

ATAC-seq: Assay for transposase-accessible chromatin using sequencing

bp: Base pair

BCF: Binary variant call format (binary version of VCF)

CAGE: Cap analysis of gene expression

CAGI: Critical assessment of genome interpretation

CCLE: Cancer cell line encyclopedia

CePIN: Co-expressed protein interaction network

ceRNA: Competitive endogeneous RNA

CGC: Cancer gene census

CGI: CpG island

ChIA: Chromatin interaction analysis

ChIA-PET: Chromatin interaction analysis by paired-end tag sequencing

ChIP: Chromatin immunoprecipitation (for the analysis of histone modifications)

ChIP-seq: Chromatin immunoprecipitation with massively parallel DNA sequencing

ChIRP: Chromatin isolation by RNA purification (ChIP for studying RNA)

circRNA: Circular RNA

cis-eQTL: Local cis-acting eQTL

cLIP: UV Cross-linking and immunoprecipitation

COBRA: Combined bisulfite restriction analysis

COSMIC: Catalogue of somatic mutations in cancer

CPD: Compensated pathogenic deviation

CRE: Cis-regulatory elements

CRISPR: Clustered regularly interspaced short palindromic repeats

CRM: Cis-regulatory modules

CTCF: CCCTC-binding factor

DCC: Dosage Compensation Complex

DEG: Differentially expressed genes

DHS: DNase I hypersensitivity site (also DNase HS)

DMH: Differential methylation hybridization

DMR: Differentially methylated regions

DNase HS (also DHS): DNase hypersensitive site

DNase-seq: DNase I hypersensitivity analysis coupled with high-throughput sequencing

DNMTs: DNA methyltransferases

DSB: DNA double strand break

DsiRNA: Dicer-substrate RNAs

dsRNA: Double-stranded RNA

ENCODE: ENCyclopedia Of DNA Elements

EPU: (linked) Enhancer-promoter units

eQTL: Expression quantitative trait loci (variants associated with expression levels)

Types of eQTLs:

dsQTL: DNase I sensitivity quantitative trait loci

enhSNP: enhancer SNP

esQTL: expression-specific QTLs (greater correlation with mRNA than protein abundance)

hQTL: histone-modification quantitative trait loci

haQTL: histone acetylation level quantitative trait loci

meQTL: methylation level quantitative trait loci

miR-eQTL: miRNA expression level quantitative trait loci

rQTL: ribosome occupancy quantitative trait loci

pQTL: protein abundance quantitative trait loci

psQTL: protein-specific QTLs (greater correlation with protein than mRNA abundance)

RdQTL: RNA decay quantitative trait loci

   sQTL: Splicing quantitative trait loci

eRNA: Enhancer RNA

eSNP: Expression SNP (SNPs with eQTL effects)

EWAS: Epigenome-wide association studies OR environment-wide association study

FAIRE: Formaldehyde-assisted isolation of regulatory elements

FANTOM5: Functional Annotation of the Mammalian Genome Project (phase 5)

FDR: False discovery rate

FISH: Fluorescence in situ hybridization

FPKM:   Fragments per kilobase of exon model per million mapped reads

GERP: Genomic evolutionary rate profiling

GENEVA: Gene Environment Association Studies

GFF: General feature format

GO: Gene Ontology

GSEA:   Gene set enrichment analysis

GTF: Gene transfer format

GWAS: Genome-wide association study

H3K4me: Histone 3 lysine 4 methylation

H3K4me1: Histone 3 lysine 4 monomethylation

H3K4me3: Histone 3 lysine 4 trimethylation

H3K27ac: Histyone 3 lysine 27 acetylation

HATs: Histone acetyltransferases

HDAC: Histone deacetylatase

HELP: HpaII tiny fragment enrichment by ligation-mediated PCR

HGMD: Human gene mutation database

HGVD: Human genetic variation database

Hi-C: High throughput chromosome conformation capture

HLA: Human leukocyte antigen

HMM: Hidden Markov model

HMTs: Histone methyltransferases

HPRD: Human Protein Reference Database

HRM: High resolution melting analysis

HTS: High-throughput sequencing

ICGC: International cancer genome consortium

IGV: Integrative Genomics Viewer

IMA: Illumina methylation analyzer

IM-PET: Integrated methods for predicting enhancer targets

INDELs: Insertions and Deletions

kb: Kilobases

LCL: Lymphoblastoid cell line

LD: Linkage disequilibrium

lncRNA: Long non-coding RNA

lincRNA: Large intergenic non-coding RNAs

lincRNA cis-eQTLs: SNPs affecting lincRNA expression

LOESS: Locally weighted scatterplot smoothing

LOF: Loss of function

LSD1: Lysine-specific histone demethylase KDM1A

MACS: Model-based analysis of ChIP-seq

MAF: Minor allele frequency

MAP: Mean average precision

Mb: Megabases

MBD: Methyl-CpG binding domain

MeCP: Methyl-CpG binding protein

MeDIP methylated DNA immunoprecipitation

MCEV: Multiple co-operative enhancer variants (see also MEV)

MeCP2: Methyl CpG binding protein 2 (along with MeCP2, MBD1, MBD2, MBD3, and MBD4  are characterized by the presence in each of a methyl-CpG binding domain (MBD).

meDIP: Methylated DNA ImmunoPrecipitation

meQTL (or metQTL): Methylation quantitative trait loci (variants associated with methylation levels), also called QTLepi (epigenetic quantitative trait loci)

MEV: Multiple enhancer variants (see also MCEV)

MHC: Major histocompatibility complex

MIME: Mutational interference mapping experiment

MIRA: Methylated CpG island recovery assay

miRISC: miRNA-induced silencing complex

miRNP: miRNA ribonucleoprotein complexes

MPS: Massive parallel sequencing

MRE: microRNA response/recognition elements

mRNA-seq: Messenger RNA abundance measured by high-throughput sequencing

MSA: Multiple sequence alignment

MS-SnuPE: Methylation-sensitive single nucleotide primer extension

MS-SCCA: Methylation-sensitive single strand conformation analysis

MSSC: Methylation-sensitive cut counting assay

MSP: Methylation-specific PCR (see also qAMP)

ncRNA: Non-coding RNA

nsSNP: non-synonymous SNP

NGS: Next-generation sequencing

PARs: Promoter-associated RNAs

PBMC: peripheral blood mononuclear cell

PCA: Principal component analysis

PCC: Pearson correlation coefficient

PCR: Polymerase chain reaction

PDB: Protein data bank

PE read: Paired-end read

PET: Paired-end tags (5′ methyl cap and a poly(A) tail)

phosSNP: phosphorylation-related SNP

PIC: Promoter initiation complex

PICS: Probabilistic identification of causal SNPs

PIN: Protein interaction network

piRNAs: Piwi-interacting RNAs

PMCA: Phylogenetic module complexity analysis

poly-A: homopolymer A

poly-C: homopolymer C

poly-G: homopolymer G

poly-T: homopolymer T

poly-A/T: homopolymer A or T

PPI: Protein-protein interaction

pQTL: Protein quantitative trait locus

PRC: Polycomb repressive complexes

PreSTIGE: Predicting specific tissue interactions of genes and enhancers

PTGR: Post‑transcriptional gene regulation

PTM: post-translational modification

PTV: Protein truncating variant

Pu-seq: Polymerase usage sequencing

PWAS: Proteome-wide analysis of SNPs

PWM: Position weight matrix

qAMP: Quantitative analysis by methylation-specific PCR (MSP)

qPCR: Quantitative polymerase chain reaction

QTL: Quantitative trait locus

R: Open source data management and analysis package

RBPs: RNA-binding proteins

Reg SNP: Regulatory SNP (also rSNP)

REMC: Roadmap epigenomics mapping consortium

RIDGEs: Regions of increased gene expression

RIP: RNA immunoprecipitation

RISC: RNA-induced silencing complex

RMA: Robust multi-array average

RNA-PET: RNA sequencing following capture by paired end tags

RNA-seq: RNA sequencing

RBP: RNA-binding protein

RPKM: Reads per kilobase per million mapped reads (quantity of gene expression in RNA-seq)

RRBS: Reduced representation bisulphite sequencing

rRNA: Ribosomal RNA

RS: Rejection substitution (score)

RSEM: RNA-Seq by expectation maximization

RVAS: Rare variant association studies

SAGE: Serial analysis of gene expression

SAV: Single amino acid variant

scATAC-seq: Single cell assay for transposase-accessible chromatin using sequencing

scRNA-seq: Single-cell RNA-seq

SE read: Single-end read (as opposed to PE read)

SEV: Single enhancer variant

sgRNA: Single guide RNA (used in CRISPR-Cas9)

SIFT: Sorts intolerant from tolerant substitutions

siRNA: Small interfering RNAs

siSNP: Statistically indistinguishable single nucleotide polymorphisms

SM: Somatic mutation

SMRT: Single molecule, real-time (sequencing)

SNP: Single nucleotide polymorphism

SNV: Single nucleotide variant

somaMiR: Somatic mutations located within miRNAs or their target site

SRA: Sequence read archive (an NCBI database)

sRNA: Small RNA

ssSNP: Statistically similar single nucleotide polymorphisms

STR: Short tandem repeats

SVM: Support Vector Machine

TADs: Topologically associating domains

TALE: Transcription activator-like effector

TALEN: TALE-based nuclease

TAS: Trait-associated SNP

TCGA: The cancer genome atlas

TEC: To be experimentally confirmed

SNPs Single Nucleotide Polymorphisms

TET: Ten-eleven translocation

TF: Transcription factor

TFBS: Transcription factor binding site

TFRN: Transcription factor-related network

TPM: (Normalized) tags per million

trans-eQTL: Distal trans-acting eQTL

trans-cluster (eQTL hotspot): Multiple genes regulated by a single trans-eQTL

TRNs: Transcriptional regulatory networks

TSC: Transcription start cluster

TSR: Transcription start region

TSS: Transcription start site

TUCP: Transcript of uncertain coding potential

TUNEL: Terminal deoxynucleotidyl transferase dUTP nick end-labeling

UCSC: University of California Santa Cruz

UCEs: Ultraconserved elements

UHRF: Ubiquitin plant homeodomain RING finger

UTR: Untranslated region

VCF: Variant call format

VEP: Variant effect predictor

VMS: Variable methylation site

VSE: Variant set enrichment

WGBS: whole-genome bisulphite sequencing

WGS: Whole genome sequencing

WGSA: Whole-genome shotgun sequencing and assembly

WES: Whole exome sequencing

ZFN: Zinc finger-based nuclease

ZFP: Zinc finger protein

 

 

Mehmet Tevfik Dorak, M.D., Ph.D.

 Genetics      Biostatistics      HLA      MHC     Glossary      Homepage

 

12 November 2016