FeatureType

functional conservation mapping

Mapping of functionally conserved regions across species.

functional conservation quantifications

Quantification of functional conservation scores.

miRNA annotations

Annotation tracks for microRNA genes and precursors.

repeat elements annotation

Annotation of repetitive element locations and classes.

restriction enzyme site locations

Genomic positions of restriction enzyme recognition sites.

RNA-binding protein associated mRNAs

mRNAs co-immunoprecipitated with RNA-binding proteins.

splice junctions

Splice site junctions identified from RNA-seq alignments.

← transcriptome alignments

transcribed fragments

Genomic regions identified as transcribed from RNA-seq data.

transcriptome annotations

Comprehensive gene and transcript annotations for a genome.

transposable element TF ancestral origin percent by motif

Percentage of TF motif instances with transposable element ancestral origin.

transposable element TF ancestral origin percent by subfamily

Percentage of TF binding sites by TE subfamily ancestral origin.

footprints

Short protected regions within open chromatin indicating transcription factor occupancy, identified as local signal minima within peaks.

← DHS peaks, nuclease cleavage frequency

open chromatin regions

Genomic regions of accessible chromatin from ATAC-seq, DNase-seq, or similar assays.

← peaks, DHS peaks, hotspots

chromatin stripes

Elongated features in contact matrices extending from loop anchors, indicating active loop extrusion.

contact domains

Topologically associating domains (TADs) from contact matrix analysis, representing self-interacting chromatin regions.

← contact matrix

genome compartments

Large-scale A (active) and B (inactive) chromatin compartments from PCA of Hi-C contact matrices.

← contact matrix

genome subcompartments

Fine-grained chromatin compartments (A1, A2, B1, B2, B3, B4) within major A/B compartments.

loops

Chromatin loop interactions (point-to-point contacts) from contact matrices, often connecting enhancers to promoters.

← contact matrix

nested contact domains

Hierarchically nested topological domains showing multi-scale chromatin organization.

CpG sites coverage

Sequencing read coverage at CpG positions, indicating measurement confidence.

methylated reads

Reads containing DNA methylation marks from bisulfite or direct detection methods.

methylation state at CHG

DNA methylation status at CHG sequence context (H = A, C, or T), common in plant genomes.

methylation state at CHH

DNA methylation status at CHH sequence context, representing asymmetric non-CpG methylation.

methylation state at CpG

DNA methylation status (methylated/unmethylated fraction) at CpG dinucleotides, the primary context for mammalian methylation.

← methylated reads

smoothed methylation state at CpG

CpG methylation values smoothed across neighboring sites to reduce noise.

element gene interactions p-value

Statistical significance of element-gene interaction associations.

element gene interactions signal

Signal strength of element-gene interaction associations.

element gene links

Associations linking regulatory elements (commonly enhancers) to their putative target genes.

topic gene weights

Gene weights derived from topic modeling of regulatory data.

links

Generic regulatory links associating genomic elements with target features.

maternal haplotype mapping

Sequence reads or contigs assigned to the maternal haplotype.

paternal haplotype mapping

Sequence reads or contigs assigned to the paternal haplotype.

mapping

Sequence reads or contigs assigned to a haplotype.

candidate Cis-Regulatory Elements

Computationally predicted cis-regulatory elements (CREs) including enhancers, promoters, and insulators from chromatin accessibility and histone data.

candidate enhancers

Computationally predicted enhancer elements based on chromatin signatures (H3K4me1, H3K27ac, accessibility).

candidate promoters

Computationally predicted promoter elements based on chromatin signatures and TSS proximity.

curated binding sites

Manually curated and validated transcription factor binding sites.

enhancer validation

Experimental validation data for predicted enhancers.

enhancers reference

Reference set of annotated enhancer elements.

polyA sites

Polyadenylation signal sites where pre-mRNA is cleaved and polyadenylated.

predicted enhancers

Computationally predicted enhancer elements.

promoters reference

Reference set of annotated promoter elements.

regulatory elements

General annotation of regulatory elements: enhancers, promoters, silencers, and insulators.

transcription start sites

Experimentally determined transcription start sites (TSS) from CAGE, PRO-seq, or similar assays.

← peaks, bidirectional peaks

TSS reference

Reference set of transcription start sites.

relative replication signal

Replication timing signal expressed relative to a reference.

replication timing profile

Genome-wide profile of DNA replication timing.

Nm methylation state

2′-O-methylation (Nm) modification.

inosine methylation state

Inosine (A-to-I editing) modification.

m5C methylation state

5-methylcytosine (m5C) RNA modification.

m6A methylation state

N6-methyladenosine (m6A) modification on transcripts. m6A is the most abundant internal mRNA modification.

pseudouridine methylation state

Pseudouridine (Ψ) modification. Pseudouridine is the most abundant RNA modification.

PWMs

Position weight matrices representing sequence motif models, encoding nucleotide preferences at each position.

sequence motifs

Sequence patterns enriched in genomic regions of interest.

sequence motifs instances

Genomic locations where specific sequence motifs occur.

sequence motifs report

Summary report of motif discovery or enrichment analysis.

cell type annotations

Cell type labels assigned to individual cells based on marker genes or reference mapping.

← clusters

cell type data

Data associated with cell type identity in single-cell experiments.

3D structure

Three-dimensional structural model of a genomic region or chromatin domain.

contigs

Assembled sequence contigs from genome assembly.

personalized genome assembly

Genome assembly incorporating an individual's sequence variation.

predicted 3D structural ensembles

Computationally predicted ensembles of 3D genomic structures.

allele-specific variants

Variants showing allele-specific behavior in expression or chromatin accessibility.

copy number variation

Genomic regions with altered copy numbers (deletions, duplications) relative to reference.

curated SNVs

Manually curated and validated single nucleotide variants.

dsQTLs

DNase I sensitivity quantitative trait loci: variants associated with chromatin accessibility.

eQTLs

Expression quantitative trait loci: variants statistically associated with gene expression levels.

maternal variant calls

Variants called specifically from the maternal haplotype.

paternal variant calls

Variants called specifically from the paternal haplotype.

reference variants

Variants relative to a reference genome.

variant calls

Called genomic variants (SNPs, indels, structural variants) in VCF format.

variant effect quantifications

Quantitative measurements of variant functional effects.

variant reference

Reference database or set of known genomic variants.

SNPs

Single nucleotide polymorphisms.

indels

Insertion/deletion variants.