187_ES_JM8.N4_Mitosis_A

In [1]:

# Parameters
sample_name = "ES;JM8.N4;Mitosis;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_187-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_187-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 00:50:04,520 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	JM8.N4 Mitosis
Cell Group	ES cells and embryonic tissues
Experiment Name	ATAC
Experiment Group	GEO

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	121173	75150	3.9409	145556657	5190019	0.0357	7256741	0.0499	46929464	0.3225
rep2	121173	75150	3.54	186466550	5825601	0.0312	8392411	0.045	58666393	0.3147

Modelling Metadata

Metric	Value
auPRC	0.6752
Calibrated Recall at 50% FDR	0.219
Number of Positive Examples in Test Data	29932
Number of Negative Examples in Test Data	8040919
Imbalance Ratio in Test Data	0.0037
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
Sox2
Tcfeb
Pbx3

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Sp2		absent
Fos		absent
Rest		absent
Rfx2		absent
Rfx8		absent
Mbtps2		absent
Ets1		absent
Creb3		absent
Grhl1		absent
Hsf1		absent
Smarcc2		absent
Ctcfl		absent
Sp3		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Zfp143	absent
Gabpa	absent
E2f1	absent
Klf14	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_187-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_187-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_187-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_0, # patterns: 28, # seqlets: 20440, Positive for: ES;JM8.N4;Mitosis;A;GEO

pattern_0: # seqlets: 3829
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp2 , Sp3 , Zbtb7a , Klf5 , Sp5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 2337
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1822
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcfl , Ctcf
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1654
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1469
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp2 , Sp3 , Zfp281 , Klf5 , Zfp148
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1406
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ets1 , Gabpa , Etv4 , Erf , Etv1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 1096
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sox2 , Pou5f1 , Tbpl2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 870
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sox2 , Pou5f1 , Sox30 , Sry , Sox4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 799
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Sp3 , Yy1 , Wt1 , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 763
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 744
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Creb3 , Jdp2 , Atf7 , 9430076C15Rik , Atf2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 505
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfeb , Bach2 , Tcfec , Mitf , Tcfe3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 452
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 407
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx2 , Rfx1 , Arid2 , Sp3 , Rfx4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 397
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Smarcc1 , Bach1 , Nfe2 , Fosb
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 298
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx8 , Rfx3 , Rfx5 , Rfx4 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 254
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 248
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Zfx , Tcfap2d , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 192
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Klf5 , Maz , Klf15
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 172
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 154
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , E2f1 , Zfx , Zbtb7a , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_21: # seqlets: 154
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_22: # seqlets: 84
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rest , Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_23: # seqlets: 83
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_24: # seqlets: 80
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , E2f1 , Zbtb7a , Wt1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_25: # seqlets: 67
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rest , Sp3 , Zbtb7a , Wt1 , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_26: # seqlets: 64
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Grhl1 , Tcfcp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_27: # seqlets: 40
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , E2f1 , Zbtb7a , Wt1 , Ctcfl
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_187-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_187-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_187-naivegw

No motifs with negative importance