Genome Biology Genetics Biostatistics R HLA MHC Glossary Homepage
Genome Biology Abbreviations
1KG: One thousand genome study
3C: Chromosome conformation capture (a chromatin looping assay)
4C: Circular chromosome conformation capture / chromosome conformation capture-on-chip (a chromatin looping assay)
4C-seq: Circular chromosome conformation capture followed by sequencing
5C: Chromosome conformation capture carbon copy (a chromatin looping assay)
6C: Combined 3C-ChIP-cloning (a chromatin looping assay)
5-hmC: 5-hydroxymethylcytosine
5-mC: 5-methylcytosine
A2I: Adenosine to Inosine (RNA editing)
AAS: Amino acid substitution
ADAR: Adenosine deaminases acting on RNA (RNA editing)
AIC: Akaike information criterion
APA: Alternative polyadenylation
APBSs: High occupancy architectural protein binding sites
API: Application programming interface
AR: Androgen receptor
ASE: Allele-specific expression
ASM: Alternative splicing module
ASO: Antisense oligonucleotides
ATAC-seq: Assay for transposase-accessible chromatin using sequencing
AUROC: Area under the receiver operating characteristic curve
AUPR: Area under the precision-recall curve
bp: Base pair
BCF: Binary variant call format (binary version of VCF)
CAGE: Cap analysis of gene expression
CAGI: Critical assessment of genome interpretation
CAGE: Cap analysis of gene expression; Consortium for the Architecture of Gene Expression
CCD: Chromatin contact domains
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 (a chromatin looping assay)
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)
ChromEMT: Chromatin electron microscopy tomography
circRNA: Circular RNA
cis-eQTL: Local cis-acting eQTL (usually within 5Mb)
CIT: Causal inference test
cLIP: UV Cross-linking and immunoprecipitation
CLIP-seq: Crosslinking immunoprecipitation-seq
COBRA: Combined bisulfite restriction analysis
COJO: Conditional and joint stepwise model selection
COSMIC: Catalogue of somatic mutations in cancer
CPD: Compensated pathogenic deviation
CRCs: Chromatin remodeling complexes
CRE: Cis-regulatory elements
CRE-seq: Cis-regulatory element analysis by sequencing
CRISPR: Clustered regularly interspaced short palindromic repeats
CRM: Cis-regulatory modules
CSRE: Cell type-specific regulatory elements
CTCF: CCCTC-binding factor
CWAS: Coding-Wide Association Studies
daVs: Disease-associated variants
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
DPE: Downstream promoter element (typically 20-30bp downstream of TSS)
DSB: DNA double strand break
DsiRNA: Dicer-substrate RNAs
dsRNA: Double-stranded RNA
EFO: Experimental factor ontology
eGTEx: Enhancing GTEx Project
EIS: Enhancer interaction signal
EMS: Expression modifier score
ENCODE: ENCyclopedia Of DNA Elements
E-P: Enhancer-promoter
EPI: Enhancer-promoter interaction
epi-RILs: Epigenetic recombinant inbred lines
EPRI: Enhancer–promoter RNA interaction
EPU: (linked) Enhancer-promoter units
eQTL: Expression quantitative trait loci (variants associated with expression levels)
Types of eQTLs:
3'aQTL: 3'-untranslated region alternative polyadenylation QTL
aseQTL: allele-specific expression QTL
bQTL: (Transcription factor) binding QTL
caQTL: chromatin accessibility QTL
cdsQTLs: variants affecting expression of open reading frame
co-eQTL: co-expression QTLs (link)
deSNP: deleterious enhancer SNP
dsQTL: DNase I sensitivity quantitative trait loci
eaQTL: enhancer activity QTL
edQTL: RNA-editing QTL
elncRNA: eQTL lncRNA
enhSNP: enhancer SNP
eQTM: expression quantitative trait methylation
eQTN: expression quantitative trait nucleotide (causative eQTL)
esQTL: expression-specific QTLs (greater correlation with mRNA than protein abundance)
hQTL: histone-modification quantitative trait loci
haQTL: histone acetylation level quantitative trait loci
isoQTL: variants affecting expression of specific transcript isoforms
lncR-eQTLs: lncRNA eQTLs
meQTL: methylation level quantitative trait loci
miR-eQTL: miRNA expression level quantitative trait loci
pieQTLs: promoter-interacting expression quantitative trait loci
pQTL: protein abundance quantitative trait loci
psQTL: protein-specific QTLs (greater correlation with protein than mRNA abundance)
puQTL: promoter usage QTL
rbSNP: RNA-binding protein binding site SNP
RdQTL: RNA decay quantitative trait loci
RNAe-QTL: RNA editing quantitative trait loci
QTLepi: epigenetic quantitative trait loci (correlations with DMR)
rQTL: ribosome occupancy quantitative trait loci
reQTL: response eQTL
sQTL: splicing QTL (or ssQTL for splice-site QTL)
tssQTLs: variants affecting expression of transcription start sites
eRNA: (Non-coding) enhancer RNA
eSNP: Expression SNP (SNPs with eQTL effects)
ESP: Exome sequencing project
EVS: Exome variant server
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
FIREs: Frequently Interacting REgions
FISH: Fluorescence in situ hybridization
FPKM: Fragments per kilobase of exon model per million mapped reads
F-SNP: Follower SNP (equivalent to siSNP/ssSNP)
G2N: Genes2Networks
GEO: Gene Expression Omnibus
GERP: Genomic evolutionary rate profiling
GENEVA: Gene Environment Association Studies
GFF: General feature format
GO: Gene ontology
GRO-seq: Global nuclear run-on sequencing
GROMIT: Genome regulatory organization mapping with integrated transposons
GRR: Genomic risk region (the region spanned by the ssSNP set)
GSEA: Gene set enrichment analysis
GTF: Gene transfer format; general transcription factor
GWAS: Genome-wide association study
GWAX: GWAS by proxy (the phenotype is inferred on the basis of parental phenotype)
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
HMs: Histone modifications
HMM: Hidden Markov model
HMTs: Histone methyltransferases
hnRNP: Heterogeneous nuclear ribonucleoprotein
HPRD: Human Protein Reference Database
HRM: High resolution melting analysis
HTS: High-throughput sequencing
ICGC: International Cancer Genome Consortium
iCHAVs : Correlated, highly trait-associated variants
IGV: Integrative Genomics Viewer
IMA: Illumina methylation analyzer
IM-PET: Integrated methods for predicting enhancer targets
INDELs: Insertions and Deletions
kb: Kilobases
KEA: Kinase Enrichment Analysis
KEGG: Kyoto encyclopedia of genes and genomes
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
LRES: Long-range epigenetic silencing
LSD1: Lysine-specific histone demethylase KDM1A
L-SNP: Lead SNP (see also F-SNP)
MACS: Model-based analysis of ChIP-seq
MAF: Minor allele frequency
MAP: Mean average precision
Mb: Megabases
MBD: Methyl-CpG binding domain
ME: Metastable epiallele
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
mmPCR-seq: Microfluidic multiplex PCR followed by deep sequencing
MNase-seq: Sequencing of micrococcal nuclease sensitive sites
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
nRIP-seq: Native RNA immunoprecipitation (nRIP) coupled with high-throughput sequencing (ref)
nsSNP: non-synonymous SNP
NGS: Next-generation sequencing
NMD: Nonsense-mediated mRNA decay
NOMe-seq: Nucleosome Occupancy and Methylome sequencing
ORA: Over-representation analysis
PARs: Promoter-associated RNAs
PAV: Protein-altering variant
PBMC: Peripheral blood mononuclear cell
PCA: Principal component analysis
PCC: Pearson correlation coefficient
PCHi-C: Promoter capture Hi-C
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)
PheWAS: Phenome-wide association study
phosSNP: phosphorylation-related SNP
PIC: Promoter initiation complex; pre-initiation complex
PICS: Probabilistic identification of causal SNPs
PIN: Protein interaction network
PIR: Promoter interacting region
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
PRD: Protein-RNA difference (because of splicing/post-translational modifications etc)
PreSTIGE: Predicting specific tissue interactions of genes and enhancers
PROMPT: promoter upstream transcripts
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
qRRM: Quasi RNA recognition motif
QTL: Quantitative trait locus
R: Open source data management and analysis package
RDD: RNA-DNA difference (as a result of RNA editing)
RBD: RNA-binding domain
RBP: RNA-binding protein
RGG box: Arg-Gly-Gly box
Reg SNP: Regulatory SNP (also rSNP)
REMC: Roadmap epigenomics mapping consortium
REST: Representational state transfer
RiboSNitch: A genetic variant that alter RNA structure
RIDGEs: Regions of increased gene expression
RIP: RNA immunoprecipitation
RISC: RNA-induced silencing complex
RL: Regulatory landscapes
RMA: Robust multi-array average
RNAe: RNA editing
RNA-PET: RNA sequencing following capture by paired end tags
RNA-seq: RNA sequencing
RNA TRAP: RNA tagging and recovery of associated proteins
RNP: Ribonucleoprotein
ROA: Resource oriented architecture
ROSE: Rank Ordering of Super-Enhancers
RPKM: Reads per kilobase per million mapped reads (quantity of gene expression in RNA-seq)
RRBS: Reduced representation bisulphite sequencing
RRM: RNA recognition motif
rRNA: Ribosomal RNA
RS: Rejection substitution (score)
RSEM: RNA-Seq by expectation maximization
RSS: Recursive splicing site
RVAS: Rare variant association studies
rWGCNA: Robust weighted gene coexpression network analysis
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
SLM: SNP-lncRNA-mRNA
SM: Somatic mutation
SMR: Summary-based Mendelian randomisation
SMRT: Single molecule, real-time (sequencing)
SNP: Single nucleotide polymorphism
snRNP: Small nuclear ribonucleoprotein
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
STARR-seq: Self-Transcribing Active Regulatory Regions sequencing
STR: Short tandem repeats
SVM: Support Vector Machine
T2C: Targeted Chromatin Capture
T2T: Telomer-to-telomer sequencing
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
TET: Ten-eleven translocation
TF: Transcription factor
TFBS: Transcription factor binding site
TFRN: Transcription factor-related network
TIS: Translation initiation site
TssAFlnk: Flanking active transcription start site
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
uaRNA: promoter upstream antisense RNAs
UCSC: University of California Santa Cruz
UCEs: Ultraconserved elements
UHRF: Ubiquitin plant homeodomain RING finger
UMI: Unique molecular identifiers
UMI-4C: A technique that combines chromosome conformation capture (4C) and unique molecular identifiers (UMI)
UTR: Untranslated region
X2G: Expression2Kinases
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
Genome Biology Genetics Biostatistics R HLA MHC Glossary Homepage
16 August 2023