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HMM Prediction of D. melanogaster Chromatin States

experiment: HMM Prediction of D. melanogaster Chromatin States project: Chromosomal Proteins PI: Gary Karpen Labs: Gary Karpen
Multiple histone modifications act in concert to determine genome functions, producing combinatorial chromatin ?states?. We used unsupervised, multivariate HMM machine learning to segment the genome based on the combinatorial patterns of 18 histone modifications in S2 and BG3 cells (52). This produced a nine state intensity-based model (continuous model states c1 to c9) reflecting major chromatin states, as well as a 30 state model that identifies combinatorial patterns at a finer resolution (discrete model states d1 to d30).

All features generated by this experiment:
Feature Export
ChromatinState 189618
This represents 179023 unique ChromatinStates
TAB CSV GFF3 (for UCSC) SEQ
All GBrowse tracks generated for this experiment:
GBrowse tracks: by chromosome
There are 4 Computational annotation submissions for this experiment:
DCC id Name cell line Embargoed until Features, GBrowse and Data Files
modENCODE_3365


Related to: modENCODE_2655
modENCODE_290
modENCODE_292
modENCODE_294
modENCODE_296
modENCODE_298
modENCODE_303
modENCODE_304
modENCODE_305
modENCODE_307
modENCODE_309
modENCODE_311
modENCODE_313
modENCODE_3170
modENCODE_319
modENCODE_3300
modENCODE_3304
modENCODE_963

30-State Chromatin Annotation in Drosophila.S2 S2-DRSC [ALL]
embargo expired
ChromatinState: 74186   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: 30STATE_S2


18 files Download data files
modENCODE_3363


Related to: modENCODE_2655
modENCODE_290
modENCODE_292
modENCODE_294
modENCODE_296
modENCODE_298
modENCODE_303
modENCODE_304
modENCODE_305
modENCODE_307
modENCODE_309
modENCODE_311
modENCODE_313
modENCODE_3170
modENCODE_319
modENCODE_3300
modENCODE_3304
modENCODE_963

9-State Chromatin Annotation in Drosophila.S2 S2-DRSC [ALL]
embargo expired
ChromatinState: 21955   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: 9STATE_S2


18 files Download data files
modENCODE_3364


Related to: modENCODE_2653
modENCODE_2654
modENCODE_288
modENCODE_291
modENCODE_293
modENCODE_295
modENCODE_297
modENCODE_299
modENCODE_3005
modENCODE_301
modENCODE_306
modENCODE_310
modENCODE_312
modENCODE_316
modENCODE_3299
modENCODE_3303
modENCODE_967

30-State Chromatin Annotation in Drosophila.BG3 ML-DmBG3-c2 [ALL]
embargo expired
ChromatinState: 72743   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: 30STATE_BG3


17 files Download data files
modENCODE_3362


Related to: modENCODE_2653
modENCODE_2654
modENCODE_288
modENCODE_291
modENCODE_293
modENCODE_295
modENCODE_297
modENCODE_299
modENCODE_3005
modENCODE_301
modENCODE_306
modENCODE_310
modENCODE_312
modENCODE_316
modENCODE_3299
modENCODE_3303
modENCODE_967

9-State Chromatin Annotation in Drosophila.BG3 ML-DmBG3-c2 [ALL]
embargo expired
ChromatinState: 20734   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: 9STATE_BG3


17 files Download data files