100_ES_F1216_A

In [1]:

# Parameters
sample_name = "ES;F1216;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_100-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_100-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 20:12:48,038 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	mouse embryonic stem cells (F1216)
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	148115	95272	9.1871	75743004	10188192	0.1345	7426944	0.0981	28133260	0.3715

Modelling Metadata

Metric	Value
auPRC	0.6992
Calibrated Recall at 50% FDR	0.144
Number of Positive Examples in Test Data	86037
Number of Negative Examples in Test Data	7984814
Imbalance Ratio in Test Data	0.0107
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
Ctcf
Rest
Pbx3
Pou5f1
Sp3
Gabpa

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Creb3		absent
Sox4		absent
Smarcc2		absent
Grhl1		absent
Zfp281		absent
Rfx1		absent
Mbtps2		absent
Figla		absent
Zfx		absent
Smarcc1		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Zfp143	absent
Atf7	absent
Arntl	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_100-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_100-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_100-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_0, # patterns: 21, # seqlets: 13449, Positive for: ES;F1216;A;GEO

pattern_0: # seqlets: 2145
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 2144
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Zbtb7a , Maz , Klf16
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 2004
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , E2f1 , Wt1 , Zfx , Sp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1093
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zfp281 , Zfp148 , Sp2 , Sp3 , Maz
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 922
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 646
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gabpa , Erf , Nr2c2 , Etv5 , Elk1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 622
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pou5f1 , Sox2 , Tbpl2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 582
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sox4 , Sox3 , Sox6 , Sox9 , Sox17
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 496
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Creb3 , 9430076C15Rik , Creb1 , Atf7 , Jdp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 477
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zfx
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 384
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 373
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc1 , Fos , Fosb , Nfe2l2 , Nfe2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 335
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Rfx2 , Arid2 , Rfx4 , Rfx5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 294
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 255
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Sp3 , Yy1 , Wt1 , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 231
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 123
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 116
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rest
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 81
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rest
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 77
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Grhl1 , Tcfcp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 49
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Figla
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_100-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_100-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_100-naivegw

No motifs with negative importance