In [1]:
# Parameters
sample_name = "KDNY;8wks;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_223-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_223-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 02:35:29,328 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeKidney(adult-8wks)
    Cell GroupOther Tissues
    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
    rep12006031403218.9682104649434245930430.235103744640.0992429185560.4102
    rep220060314032115.40592369400043505310.183724437750.103296764330.4086
    Modelling Metadata
    MetricValue
    auPRC0.5502
    Calibrated Recall at 50% FDR0.248
    Number of Positive Examples in Test Data133263
    Number of Negative Examples in Test Data7937588
    Imbalance Ratio in Test Data0.0165
    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
Hnf4g
Sp3
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Dbpabsent
Pbx3absent
Nfiaabsent
Smarcc2absent
Erfabsent
Pax5absent
Mef2aabsent
Mbtps2absent
9430076C15Rikabsent
Foxc1absent
Bach1absent
Hoxc9absent
Bach2absent
Irf1absent
Rfx2absent
Hsf1absent
Grhl1absent
Unique Homer Motifs
Motif NameModiscoHomer
Srebf2absent
Zfp143absent
Elk1absent
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_223-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_223-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_223-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 25, # seqlets: 22966, Positive for: KDNY;8wks;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_223-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_223-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_223-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 27, # seqlets: 11596, Negative for: KDNY;8wks;D;En
  • pattern_0: # seqlets: 1857 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp637

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1399 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1383 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Id4, Mesp2, Twist1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1253 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ppara, Nr1h2, Esrrg, Nr4a2, Rxra

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 1093 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 966 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7a, Rreb1, Klf16, Zfp148, Zbtb7b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 802 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hic2, Hic1, Zbtb7c, Gli3, Gli1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 763 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Erg, Ets1, Fev, ENSMUSG00000044690, Elf5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 454 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfic, Nfix, Nfia, Nfib

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 324 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Fosb, Nfe2, Fos, Smarcc1, Nfe2l2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 159 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 147 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Mnt

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 101 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tcf15, Msc, Tcf21, Atoh1, Zfp238

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 92 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 91 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 98 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 72 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 82 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 65 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 71 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hoxb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 60 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 55 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 50 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Zfp143

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_23: # seqlets: 46 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_24: # seqlets: 42 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Mnt

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_25: # seqlets: 38 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_26: # seqlets: 33 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores