In [1]:
# Parameters
sample_name = "AML;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_270-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_270-naivegw/NaiveauPRC.txt"
homer_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_scans"
In [2]:
from matlas.modisco_report import modisco_report_pipeline, display_metadata
reportfile= "/mnt/lab_data/kundaje/msharmin/mouse_hem/with_tfd/full_mouse50/filtering samples_MS2.xlsx"
sheetname = "filter23"

load data from labcluster

Using TensorFlow backend.
2019-07-23 04:56:38,078 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeacute myeloid leukemia
    Cell GroupCancer or Immortalized cells
    Experiment NameDHS
    Experiment GroupENCODE
    Pipeline Output
    replicateNaïve overlap peaksIDR peaksTSS enrichment (< 8 is very poor <10 is low)Final number of unique mapping, dup-filtered, chrM filtered readsNumber of reads in called peak regionsFraction of reads in called peak regionsNumber of reads in promoter regionsFraction of reads in promoter regionsNumber of reads in enhancer regionsFraction of reads in enhancer regions
    rep11982081495225.8136241539321447683910.1854193169710.08943310200.3906
    rep219820814952218.34482781236071169750.25644854620.1613115388470.4151
    rep319820814952212.79622165500829060370.134227671690.127884820680.3918
    Modelling Metadata
    MetricValue
    auPRC0.6384
    Calibrated Recall at 50% FDR0.208
    Number of Positive Examples in Test Data130371
    Number of Negative Examples in Test Data7940480
    Imbalance Ratio in Test Data0.0162
    Test Chromosomeschr2, chr3, chr19
In [4]:
from matlas.modisco_report import display_comparative_motif_sets
display_comparative_motif_sets(sample_name, homer_root, modisco_root)

TF-MoDISco is using the TensorFlow backend.
Number of CISBP motifs obtained by TF-MoDISco and Homer-denovo
Shared Motifs
Motif NameModiscoHomer
Ctcf
Rest
Fos
Sfpi1
Mbtps2
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Mef2aabsent
Foxi1absent
Hoxa9absent
Tcfebabsent
Nfibabsent
Rfx1absent
Creb3absent
Cebpbabsent
Elk1absent
Bcl11aabsent
Smarcc2absent
Sp3absent
Gabpaabsent
Runx1absent
Unique Homer Motifs
Motif NameModiscoHomer
Cebpaabsent
Zfp143absent
Klf7absent
E4f1absent
In [5]:
modisco_report_pipeline(sample_name, modisco_root, mitra_subdir, task_dir, database_name, 
                        importance=True, render=True)

rsync -t -av /srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019/task_270-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_270-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_270-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 24, # seqlets: 28127, Positive for: AML;D;En
In [6]:
modisco_report_pipeline(sample_name, modisco_root, mitra_subdir, task_dir, database_name, 
                        importance=False, render=True)

rsync -t -av /srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019/task_270-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_270-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_270-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 13, # seqlets: 8666, Negative for: AML;D;En
  • pattern_0: # seqlets: 2265 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1808 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1517 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2, Zbtb7b, Glis1, Gli1, Gli2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1248 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Klf15, Maz, Rreb1, Sp2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 472 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Erg, Ets1, ENSMUSG00000044690, Fev, Elf5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 408 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 363 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Cebpb, Cebpa, Cebpd, Cebpg

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 214 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx1, Runx2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 100 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 79 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfe2l2, Nfe2, Fos, Jund, Batf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 88 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 52 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 52 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores