In [1]:
# Parameters
sample_name = "MEL;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_273-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_273-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 05:04:50,757 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeMEL cell line
    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
    rep121860618391411.77512191362755759880.254732424170.148195606740.4366
    rep22186061839144.3659227076119497425840.2191188670410.0831892757300.3932
    Modelling Metadata
    MetricValue
    auPRC0.5272
    Calibrated Recall at 50% FDR0.263
    Number of Positive Examples in Test Data143529
    Number of Negative Examples in Test Data7927322
    Imbalance Ratio in Test Data0.0178
    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
Nfe2l2
Pbx3
Sfpi1
Ctcf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Irf1absent
Hsf1absent
Mbtps2absent
Tcfebabsent
Runx2absent
Sp5absent
Cebpbabsent
Gata1absent
Gabpaabsent
Creb3absent
Nfibabsent
Smarcc2absent
Sp3absent
Restabsent
Unique Homer Motifs
Motif NameModiscoHomer
Gata6absent
Klf2absent
Zfp143absent
E4f1absent
E2f7absent
Yy1absent
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_273-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_273-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_273-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 20, # seqlets: 24937, Positive for: MEL;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_273-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_273-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_273-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 22, # seqlets: 9954, Negative for: MEL;D;En
  • pattern_0: # seqlets: 1948 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7a, Klf16, Sp3, Sp2, Zfp148

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1822 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Onecut1, Onecut3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1598 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 873 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata6, Gata2, Gata5, Gata3, Gata4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 763 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 499 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Erg, Sfpi1, Ets1, ENSMUSG00000044690, Elf5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 352 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx2, Runx1, Runx3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 357 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 322 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 267 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Fos, Nfe2l2, Nfe2, Smarcc1, Jund

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 196 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 176 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 108 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 109 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1, Foxm1, Foxn3, Foxp4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 92 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp281

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 92 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 83 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sox9, Sox17, Sox6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 91 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 76 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sox9

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 45 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 49 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Onecut2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 36 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores