ENCODE
    • Matrix
    • Search
    • Summary
    • Search by region
    • Reference epigenomes
    • Publications
    • About
    • Visualize (SCREEN)
    • Matrix
    • Search
    • Methods
    • Antibodies
    • Biosamples
    • Genome references
    • Standards and guidelines
    • Ontologies
    • File formats
    • Software tools
    • Pipelines
    • Release policy
    • Data access
    • Schemas
    • Getting started
    • Tutorials
    • REST API
    • Cart
    • Project overview
    • Acknowledgements
    • Contact
    • News
    • Citing ENCODE

Annotation matrix

Enter search terms to filter the annotations included in the matrix.

Annotation type
  • candidate regulatory elements
    585
  • chromatin state
    81
  • enhancer predictions
    7
  • validated enhancers
    6
  • gene expression
    5
  • transcript expression
    5
  • representative DNase hypersensitivity sites
    2
  • blacklist
    1
Date released
  • August, 2017
    316
  • August, 2016
    202
  • September, 2017
    139
  • August, 2015
  • September, 2014
    15
  • November, 2016
    7
  • April, 2017
    3
  • June, 2015
    2
  • September, 2012
    2
  • September, 2015
    2
  • February, 2015
    1
  • March, 2014
    1
  • March, 2016
    1
  • October, 2015
    1
Target(s) of assay
  • H3K4me3
    293
  • H3K27ac
    265
  • CTCF
    63
Available data
  • bed bed3+
    568
  • bigBed bed3+
    563
  • bed bed9
    77
  • bigBed bed9
    77
  • fastq
    14
  • tsv
    11
  • bed bed3
    3
  • bed candidate enhancer predictions
    2
  • bed enhancer predictions
    2
  • bed enhancerAssay
    2
  • bigBed enhancerAssay
    2
  • bed narrowPeak
    1
  • fasta
    1
Organism
  • Homo sapiens
    4951
  • Mus musculus
    692
Biosample type
  • tissue
    586
  • cell line
    53
  • primary cell
    24
  • in vitro differentiated cells
    5
Organ
  • brain
    191
  • embryo
    106
  • heart
    55
  • liver
    55
  • limb
    41
  • lung
    35
  • epithelium
    33
  • kidney
    32
  • intestine
    31
  • stomach
    26
  • spleen
    20
  • bone element
    13
  • bone marrow
    13
  • blood
    12
  • bodily fluid
    12
  • connective tissue
    12
  • thymus
    8
  • eye
    7
  • gonad
    7
  • lymph node
    7
  • small intestine
    6
  • testis
    6
  • adipose tissue
    5
  • extraembryonic component
    4
  • placenta
    4
  • spinal cord
    2
  • large intestine
    1
  • musculature of body
    1
Cell
  • stem cell
    27
  • hematopoietic cell
    13
  • myeloid cell
    13
  • B cell
    7
  • cancer cell
    7
  • fibroblast
    7
  • leukocyte
    5
  • neural cell
    3
Project
  • ENCODE
    692
Genome assembly
  • mm10
    471
  • mm9
    17
  • hg19
    2
  • mm10-minimal
    2
  • GRCh38-minimal
    1
Encyclopedia version
  • 4
    457
  • 3
    209
  • 2
    25
  • Blacklists
    1
Audit category:
  • inconsistent assembly
    28
  • missing analysis_step_run
    24
month_released!
  • August, 2015
BIOSAMPLE
TYPE

692 results

Clear Filters
candidate regulatory elements
chromatin state
enhancer predictions
validated enhancers
gene expression
transcript expression
representative DNase hypersensitivity sites
blacklist
tissue
hindbrain507
midbrain507
forebrain46711
heart45811
liver478
cell line
MEL cell line121
CH12.LX61
ES-E146
ES-Bruce441
G1E41
primary cell
bone marrow macrophage5
embryonic fibroblast5
Muller cell3
erythroblast21
megakaryocyte21
in vitro differentiated cells
acute myeloid leukemia2
erythroblast2
adipocyte1
  • Citing ENCODE
  • Privacy
  • Contact
  • Submitter sign-in
  • ENCODE
  • Stanford University

©2019 Stanford University