230_Heart_8wks_D

In [1]:

# Parameters
sample_name = "Heart;8wks;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_230-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_230-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 02:57:12,928 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	Heart (adult-8wks)
Cell Group	Other Tissues
Experiment Name	DHS
Experiment Group	ENCODE

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	216638	164862	6.7714	231063522	NA	NA	NA	NA	NA	NA

Modelling Metadata

Metric	Value
auPRC	0.5425
Calibrated Recall at 50% FDR	0.27
Number of Positive Examples in Test Data	85252
Number of Negative Examples in Test Data	7985599
Imbalance Ratio in Test Data	0.0106
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
Smarcc2
Mbtps2
Pbx3
Ctcf

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Nfia		absent
Erg		absent
Mef2c		absent
Figla		absent
Gata1		absent
Atf7		absent
Cebpb		absent
Nr4a1		absent
Hsf1		absent
Bach2		absent
Nfe2l2		absent
Rfx1		absent
Irf1		absent
Sp3		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Elk4	absent
E2f7	absent
Mef2d	absent
Tcfeb	absent
Sp5	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_230-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_230-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_230-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_0, # patterns: 20, # seqlets: 19123, Positive for: Heart;8wks;D;En

pattern_0: # seqlets: 2897
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 2675
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp5 , Sp2 , Klf16 , Klf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 2529
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Erg , Ets1 , Erf , Etv5 , Gabpa
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1553
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfia , Nfic , Nfix , Nfib , Insm1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1390
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1343
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mef2c , Mef2a , Mef2d , Mef2b
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 1022
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 1009
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Atf7 , Jdp2 , Creb3 , Atf2 , 9430076C15Rik
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 862
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Bach2 , Tcfeb , Tcfec , Mitf , Tcfe3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 741
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Sp3 , Yy1 , Wt1 , Zbtb7a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 655
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Cebpb , Cebpd , Cebpa , Cebpg , Cebpe
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 540
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Figla , Atoh1 , Tcf3 , Tcfap4 , Atoh8
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 402
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfe2l2 , Nfe2 , Jund , Fos , Smarcc1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 330
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Rfx2 , Arid2 , Rfx4 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 329
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 309
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf1 , Stat2 , Prdm1 , Irf4 , Bcl11a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 186
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr4a1 , Nr4a3 , Esrrb , Esrrg , Nr5a2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 153
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 130
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gata1 , Gata2 , Gata4 , Gata6 , Gata5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 68
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_230-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_230-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_230-naivegw

No motifs with negative importance