In [1]:
# Parameters
sample_name = "NIH3T3_FBROBLST;D;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_201-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_201-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 01:36:59,363 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typefibroblast/NIH-3T3
    Cell GroupCancer or Immortalized cells
    Experiment NameDHS
    Experiment GroupGEO
    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
    rep11787111310979.0924137641571293677230.2134139943340.1017570069560.4142
    Modelling Metadata
    MetricValue
    auPRC0.5795
    Calibrated Recall at 50% FDR0.237
    Number of Positive Examples in Test Data121403
    Number of Negative Examples in Test Data7949448
    Imbalance Ratio in Test Data0.015
    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
Pbx3
Ctcf
Rest
Fos
Creb3
Runx1
Mbtps2
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Hsf1absent
Rfx1absent
Tcfecabsent
Mef2aabsent
Nfiaabsent
Zfxabsent
Irf1absent
Bhlha15absent
Erfabsent
Smarcc2absent
Sp3absent
Cebpbabsent
Unique Homer Motifs
Motif NameModiscoHomer
Zfp238absent
Zfp143absent
Sp5absent
Elk1absent
Cebpdabsent
Nficabsent
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_201-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_201-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_201-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 22, # seqlets: 25501, Positive for: NIH3T3_FBROBLST;D;GEO
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_201-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_201-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_201-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 11, # seqlets: 5447, Negative for: NIH3T3_FBROBLST;D;GEO
  • pattern_0: # seqlets: 2493 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Dbx1, Pou4f1, Tlx2, Arid3b, Pou1f1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1297 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Snai2, Zeb1, Id4, Mesp2, Scrt2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 509 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 276 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 261 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfe2l2, Nfe2, Jund, Batf, Smarcc1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 206 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Cebpb, Cebpa, Cebpd, Cebpg, Cebpe

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 122 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ctcf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 91 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 72 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 56 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 64 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores