In [1]:
# Parameters
sample_name = "NIH3T3;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_275-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_275-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 05:12:17,896 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeNIH3T3
    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
    rep117308311577330.7691895559926759290.299418136110.202938525630.4311
    rep1017308311577313.945323520612795710.11952492200.106510581830.4524
    rep1117308311577331.4668956090229227030.306319861750.208141159200.4313
    rep1217308311577331.2051952267928881080.303919667660.206940963700.431
    rep1317308311577330.9627912465327451720.301518785260.206339301330.4316
    rep1417308311577330.8126974923229992030.308220278710.208442233340.434
    rep1517308311577331.4187954792729038210.304719783830.207641080610.4311
    rep1617308311577330.599922978227555500.299118835010.204539725960.4313
    rep1717308311577331.094955800129153740.305619772310.207341110490.431
    rep1817308311577331.1128858861025334740.295617493770.204136982570.4315
    rep1917308311577339.7467333608157240.0483768540.23631391180.4277
    rep217308311577331.1411921978127670800.300718839580.204739702750.4315
    rep2017308311577330.2899884730726369650.298718046330.204438080740.4313
    rep2117308311577331.0712942604728690170.30519447670.206740585490.4314
    rep2217308311577331.1637944192828706080.304619562250.207640634220.4312
    rep2317308311577330.8915974451530171300.310220352120.209342210420.434
    rep2417308311577320.233235967648264870.23085181310.144716394370.4578
    rep2517308311577316.21212038579746149210.226622879400.112390873800.4462
    rep317308311577330.8067955870429149030.305519776590.207341104480.4309
    rep417308311577331.0242934972028300630.303319202230.205840298370.4319
    rep517308311577330.4008945261628485860.301919477330.206540677850.4312
    rep617308311577331.0729950987328981220.305319591790.206440936730.4313
    rep717308311577330.7313896754826745250.298918217270.203638608450.4314
    rep817308311577330.8715924747927796340.301218964450.205539812850.4314
    rep917308311577330.6215871993625980880.298617688280.203337543740.4315
    Modelling Metadata
    MetricValue
    auPRC0.6002
    Calibrated Recall at 50% FDR0.219
    Number of Positive Examples in Test Data148620
    Number of Negative Examples in Test Data7922231
    Imbalance Ratio in Test Data0.0184
    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
Nfic
Nfia
Ctcf
Fos
Rest
Mbtps2
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Ets1absent
Smarcc2absent
Rfx1absent
Cebpbabsent
Sp3absent
Ebf1absent
Foxi1absent
Mef2aabsent
Irf1absent
Hsf1absent
Creb3absent
Bhlha15absent
Tcfecabsent
Srfabsent
Unique Homer Motifs
Motif NameModiscoHomer
Zfp143absent
Sp2absent
E4f1absent
Cebpgabsent
Gabpaabsent
Tbpabsent
Pbx3absent
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_275-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_275-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_275-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 25, # seqlets: 22132, Positive for: NIH3T3;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_275-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_275-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_275-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 24, # seqlets: 8153, Negative for: NIH3T3;D;En
  • pattern_0: # seqlets: 1525 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Snai2, Zeb1, Id4, Mesp2, Twist1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1061 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfic, Nfia, Nfix, Nfib, Hic1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1016 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfe2l2, Nfe2, Jund, Fos, Batf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 910 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 715 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sebox, Hoxc6, Pax6, Lhx3, Dbx1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 441 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 322 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 297 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hic2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 245 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 200 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ppara, Ppard, Nr4a3, Rxra, Nr1h2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 179 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rhox8

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 173 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Arid5a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 163 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 152 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 113 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 112 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ctcf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 97 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Cebpb, Cebpa, Cebpd, Cebpg

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 94 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 88 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Batf3, Atf7, 9430076C15Rik, Creb3, Hoxa9

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 73 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 48 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 48 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 44 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_23: # seqlets: 37 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores