97_NTRPHL_A

In [1]:

# Parameters
sample_name = "NTRPHL;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_97-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_97-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 20:04:42,392 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	Neutrophils(wt)
Cell Group	Other Immune Cells
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	55808	34115	5.7693	60712105	1741510	0.0287	2778797	0.0458	19003981	0.3131
rep2	55808	34115	5.4203	68221410	1940338	0.0284	3156179	0.0463	21738311	0.3187

Modelling Metadata

Metric	Value
auPRC	0.5895
Calibrated Recall at 50% FDR	0.253
Number of Positive Examples in Test Data	32094
Number of Negative Examples in Test Data	8038757
Imbalance Ratio in Test Data	0.004
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
Sp3
Pbx3

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Smarcc2		absent
Tcfeb		absent
Nfe2l2		absent
Gabpa		absent
9430076C15Rik		absent
Foxi1		absent
Etv6		absent
Cebpb		absent
Hsf1		absent
Irf1		absent
Mbtps2		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
E4f1	absent
Elk1	absent
Zfp143	absent
Cebpg	absent
Yy1	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_97-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_97-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_97-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_0, # patterns: 17, # seqlets: 22167, Positive for: NTRPHL;A;GEO

pattern_0: # seqlets: 3799
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Etv6 , Elk1 , Elk3 , Fli1 , Elk4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 3409
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Sp5 , Klf16 , Klf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 2655
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxi1 , Pbx3 , Nfya , Ybx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 2457
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Cebpb , Cebpa , Cebpd , Cebpg , Cebpe
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1593
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1512
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 1453
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Sp3 , Yy1 , Wt1 , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 1444
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
9430076C15Rik , Creb3 , Atf2 , Atf7 , Jdp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 692
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Zfp143 , Tbx2 , Six5 , Zfp523
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 669
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gabpa , Erf , Fev , Atf2 , Etv5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 650
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfe2l2 , Nfe2 , Bach1 , Fos , Smarcc1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 529
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfeb , Bach2 , Tcfec , Mitf , Arntl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 418
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Cebpb , Cebpe , Cebpa , Cebpd , Cebpg
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 382
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf1 , Prdm1 , Bcl11a , Stat2 , Irf2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 337
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 117
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Sp3 , Foxi1 , Maz , Sp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 51
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1
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_97-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_97-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_97-naivegw

No motifs with negative importance