104_RTN_A

In [1]:

# Parameters
sample_name = "RTN;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_104-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_104-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 20:26:31,755 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	WT retina
Cell Group	Neural Cells and 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	149877	108264	16.881	39257849	9388108	0.2392	7772426	0.1981	14482689	0.3691
rep2	149877	108264	14.309	47859418	12036971	0.2516	9712932	0.203	17959926	0.3754

Modelling Metadata

Metric	Value
auPRC	0.6368
Calibrated Recall at 50% FDR	0.185
Number of Positive Examples in Test Data	113072
Number of Negative Examples in Test Data	7957779
Imbalance Ratio in Test Data	0.014
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
Sp3
Ctcf
Tcfeb

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Crx		absent
Rfx1		absent
Sp2		absent
Atoh1		absent
Mbtps2		absent
Smarcc2		absent
Foxi1		absent
Hsf1		absent
Rfx8		absent
Jdp2		absent
Rora		absent
Mef2d		absent
Gabpa		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Maz	absent
Gsc2	absent
Hes7	absent
Erf	absent
Pbx3	absent
Zfp143	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_104-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_104-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_104-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_0, # patterns: 19, # seqlets: 24205, Positive for: RTN;A;GEO

pattern_0: # seqlets: 7997
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 3877
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Crx , Dmbx1 , Obox6 , Obox1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1669
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp2 , Sp3 , Sp5 , Klf16 , Sp8
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1501
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1196
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gabpa , Erf , Ets1 , Elk3 , Etv1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1195
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxi1 , Pbx3 , Nfya , Ybx1 , Dux
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 1073
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Atoh1 , Neurod1 , Neurod2 , Tal1 , Bhlhe22
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 776
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 763
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Yy1 , Sp3 , Wt1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 667
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rora , Rorc , Nr1d1 , Pparg , Rorb
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 647
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfeb , Bach2 , Mitf , Tcfec , Tcfe3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 621
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Jdp2 , Atf7 , Atf2 , Creb1 , 9430076C15Rik
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 593
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 484
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mef2d , Mef2b , Mef2c , Mef2a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 431
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , E2f1 , Ctcfl , Wt1 , Tcfap2d
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 262
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Arid2 , Rfx2 , Rfx4 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 240
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 140
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 73
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx8 , Rfx3 , Rfx5 , Rfx7 , Rfx4
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_104-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_104-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_104-naivegw

No motifs with negative importance