In [1]:
# Parameters
sample_name = "MEF.GATA-1-ER;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_272-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_272-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 05:02:20,536 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeMEL-GATA-1-ER 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
    rep11180428578812.79961359635037383300.275322598050.166459073100.4351
    rep21180428578821.175428365427784970.27636293120.223412257970.4351
    rep31180428578815.61081464432545251090.309430019580.205362257730.4257
    rep41180428578810.33281250865029333460.234919365660.155153564200.4289
    rep51180428578818.30837950628897760.23578116300.21516259000.4306
    Modelling Metadata
    MetricValue
    auPRC0.5226
    Calibrated Recall at 50% FDR0.224
    Number of Positive Examples in Test Data115113
    Number of Negative Examples in Test Data7955738
    Imbalance Ratio in Test Data0.0143
    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
Sp3
Sfpi1
Ctcf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Foxi1absent
Mbtps2absent
Irf1absent
Gabpaabsent
Rfx1absent
Smarcc2absent
Tcfebabsent
Gata6absent
Creb3absent
Restabsent
Nfe2l2absent
Nfibabsent
Hsf1absent
Unique Homer Motifs
Motif NameModiscoHomer
Gata1absent
Zfp143absent
Nfe2absent
Pbx3absent
Hhexabsent
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_272-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_272-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_272-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 18, # seqlets: 25341, Positive for: MEF.GATA-1-ER;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_272-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_272-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_272-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 14, # seqlets: 10287, Negative for: MEF.GATA-1-ER;D;En
  • pattern_0: # seqlets: 3354 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 2682 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Zbtb7a, Sp2, Maz, E2f1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1339 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 652 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 537 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rela

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 478 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rfx2, Rfx1, Arid2, Rfx4, Rest

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 286 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 250 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 223 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 165 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 148 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 78 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 59 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Klf1, Klf4, Klf2, Klf8, Klf12

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 36 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores