In [1]:
# Parameters
sample_name = "MCRPHG_BMD.LPD_Stmltd;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_143-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_143-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.
2019-07-22 22:20:25,525 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typebone marrow-derived macrophages(Lipid A stimulation 120min)
    Cell GroupOther Immune Cells
    Experiment NameATAC
    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
    rep11167657519913.21271465198821672370.148114790120.101158334190.3986
    rep2116765751999.359185379676410080.07526497790.076330880770.3624
    rep31167657519914.5211762864843182260.245223688630.134577133060.438
    rep4116765751997.1732145719584657680.0328160610.056148445950.3329
    Modelling Metadata
    MetricValue
    auPRC0.5825
    Calibrated Recall at 50% FDR0.228
    Number of Positive Examples in Test Data89513
    Number of Negative Examples in Test Data7981338
    Imbalance Ratio in Test Data0.0111
    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
Creb3
Fos
Sfpi1
Smarcc2
Ctcf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Runx1absent
Sp3absent
Mbtps2absent
Cebpbabsent
Bcl11aabsent
Relabsent
Bach2absent
Tbpl2absent
Rfx1absent
Rfx8absent
Erfabsent
Hsf1absent
Unique Homer Motifs
Motif NameModiscoHomer
Tcfecabsent
Sp2absent
Cebpeabsent
Stat2absent
Relaabsent
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_143-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_143-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_143-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 21, # seqlets: 26468, Positive for: MCRPHG_BMD.LPD_Stmltd;A;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_143-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_143-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_143-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 24, # seqlets: 11614, Negative for: MCRPHG_BMD.LPD_Stmltd;A;GEO
  • pattern_0: # seqlets: 2413 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7b, Zbtb7a, Glis1, Glis2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1852 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1208 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sfpi1, Bcl11a, Spib, Spic, Ets1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1076 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Mga, Tbx4, Tcf4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 888 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bhlha15, Msc, Tcf21, Twist2, Neurog3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 780 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfe2l2, Nfe2, Jund, Batf, Fos

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 620 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 616 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gli1, Gli2, Gli3, Zbtb7b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 260 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 252 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 160 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb, Nr6a1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 154 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 149 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Egr2, Zfp740, Hif3a, Sp1, Gli2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 149 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 143 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rela, Rel, Nfkb1, Relb, Hivep1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 132 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx2, Runx1, Runx3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 132 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 128 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 109 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Cebpb, Cebpa, Cebpd, Cebpg, Cebpe

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 99 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 85 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ctcf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 77 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 77 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfib, Nfix, Nfia, Nfic

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_23: # seqlets: 55 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tbpl2

    SequenceContrib ScoresHyp_Contrib Scores