74_aB_CD180_A

In [1]:

# Parameters
sample_name = "aB;CD180;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_74-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_74-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 18:51:06,288 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	aBCD180
Cell Group	B cells
Experiment Name	ATAC
Experiment Group	Casellas Lab

Pipeline Output

replicate	Naïve overlap peaks	IDR peaks	TSS enrichment (< 8 is very poor <10 is low)	Final number of unique mapping, dup-filtered, chrM filtered reads	Number of reads in called peak regions	Fraction of reads in called peak regions	Number of reads in promoter regions	Fraction of reads in promoter regions	Number of reads in enhancer regions	Fraction of reads in enhancer regions
rep1	53221	34951	13.0333	55180944	4884833	0.0886	5014483	0.0909	17506509	0.3174

Modelling Metadata

Metric	Value
auPRC	0.6846
Calibrated Recall at 50% FDR	0.176
Number of Positive Examples in Test Data	44504
Number of Negative Examples in Test Data	8026347
Imbalance Ratio in Test Data	0.0055
Test Chromosomes	chr2, 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 Name	Modisco	Homer
Mbtps2
Pbx3
Sp3
Tbpl2
Ctcf

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Mef2a		absent
Nfia		absent
Smarcc2		absent
Tcfeb		absent
Erg		absent
Irf1		absent
Fos		absent
Sfpi1		absent
Rfx1		absent
Rela		absent
Hsf1		absent
Runx1		absent
Creb3		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Bcl11a	absent
Nfkb1	absent
Elk3	absent
E4f1	absent
Zfp143	absent
Klf1	absent

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_74-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_74-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_74-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_1, # patterns: 20, # seqlets: 23985, Positive for: aB;CD180;A;CL

pattern_0: # seqlets: 5858
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sfpi1 , Ets1 , Etv6 , Fli1 , Erg
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 4561
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Zbtb7a , Sp5 , Klf16
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 3611
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1687
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1581
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1104
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf1 , Stat2 , Prdm1 , Bcl11a , Irf4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 1095
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Sp3 , Yy1 , Wt1 , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 760
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 729
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Creb3 , Jdp2 , Atf7 , 9430076C15Rik , Batf3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 489
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rela , Relb , Nfkb1 , Hivep1 , Rel
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 462
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tbpl2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 441
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfeb , Tcfec , Bach2 , Mitf , Srebf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 377
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Rfx2 , Arid2 , Rfx4 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 349
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Runx1 , Runx2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 275
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Jund , Smarcc1 , Fosb , Nfe2l2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 192
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Erg , Ets1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 159
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mef2a , Mef2d , Mef2b , Mef2c
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 121
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 92
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 42
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfia , Nfix , Nfib
Sequence
Contrib Scores
Hyp_Contrib Scores

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_74-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_74-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_74-naivegw
Displaying motifs which has negative importances for the cell type

metacluster_0, # patterns: 24, # seqlets: 9304, Negative for: aB;CD180;A;CL

pattern_0: # seqlets: 1810
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zbtb7b , Glis2 , Glis1 , Zbtb7a , Zic5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 1389
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Dbx1 , Tlx2 , Arid3b , Sebox , Nkx6-1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1076
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 755
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zfp238 , Bhlha15 , Tcf21 , Tcf15 , Tcf4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 733
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfkb1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 648
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 612
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ppara , Nr1h4 , Nr1h2 , Esrrg , Rxra
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 589
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zeb1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 351
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gata1 , Gata4 , Gata2 , Mecom , Gata6
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 247
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxd3 , Foxj1 , Foxm1 , Foxn3 , Foxp4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 188
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pparg
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 125
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 109
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxp4 , Foxj3 , Foxp2 , Foxf2 , Foxc1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 92
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 86
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Bcl6 , Sfpi1 , Maz , Spib , Ets1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 75
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 76
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Bcl6 , Spib , Sfpi1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 76
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Bcl6
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 48
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Maz , Sp2 , Wt1 , Zbtb7a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 46
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxb1 , Foxc1 , Foxc2 , Foxa2 , Foxf2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 56
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2 , Esrrb , Nr6a1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_21: # seqlets: 44
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Bcl6 , Bcl11a , Sfpi1 , Maz
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_22: # seqlets: 40
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Twist1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_23: # seqlets: 33
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tbpl2 , Foxb1
Sequence
Contrib Scores
Hyp_Contrib Scores