56_Heart_D

In [1]:

# Parameters
sample_name = "Heart;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_56-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_56-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 17:56:44,731 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	Heart
Cell Group	Other Tissues
Experiment Name	ATAC
Experiment Group	Casellas Lab

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	130707	82136	21.4535	5954075	683659	0.1152	857769	0.1445	2123860	0.3578
rep2	130707	82136	13.2306	38502670	4998168	0.1299	4105237	0.1067	13824122	0.3592
rep3	130707	82136	15.6391	23641085	2972321	0.1258	2844689	0.1204	8491684	0.3595

Modelling Metadata

Metric	Value
auPRC	0.6195
Calibrated Recall at 50% FDR	0.21
Number of Positive Examples in Test Data	93709
Number of Negative Examples in Test Data	7977142
Imbalance Ratio in Test Data	0.0116
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
Mef2a
Tcfeb
Sp3

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Cebpb		absent
Creb3		absent
Nfia		absent
Erg		absent
Ferd3l		absent
Pbx3		absent
Fos		absent
Klf16		absent
Smarcc2		absent
Rfx1		absent
Irf1		absent
Gata2		absent
Mbtps2		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Gabpa	absent
Zfp143	absent
9430076C15Rik	absent
Smarcc1	absent
Tcf3	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_56-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_56-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_56-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_0, # patterns: 23, # seqlets: 18338, Positive for: Heart;D;En

pattern_0: # seqlets: 2263
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Erg , Ets1 , Erf , Etv5 , Gabpa
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 1936
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfia , Nfix , Nfic , Nfib , Insm1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1918
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1670
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp5 , Sp2 , Klf5 , Klf16
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1616
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mef2a , Mef2c , Mef2d , Mef2b
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1175
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Klf16 , Sp3 , Sp5 , Klf14 , Klf7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 1127
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Creb3 , 9430076C15Rik , Atf7 , Atf2 , Batf3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 1026
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 847
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ferd3l , Tcfap4 , Tcf21 , Atoh8 , Ascl2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 843
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 648
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Smarcc1 , Nfe2 , Nfe2l2 , Jund
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 595
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfeb , Bach2 , Tcfec , Mitf , Srebf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 570
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Cebpb , Cebpa , Cebpd , Cebpg , Cebpe
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 459
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Sp3 , Yy1 , Wt1 , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 289
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 259
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf1 , Stat2 , Prdm1 , Irf4 , Irf2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 227
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Rfx4 , Rfx2 , Arid2 , Rfx5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 192
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gata2 , Gata1 , Gata4 , Gata6 , Gata5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 194
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Ctcfl , Zfx , Wt1 , Sp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 187
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Wt1 , Zfx , Ctcfl , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 110
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Ctcfl , E2f1 , Wt1 , Zfx
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_21: # seqlets: 95
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , E2f1 , Ctcfl , Zfx , Zbtb7a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_22: # seqlets: 92
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
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_56-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_56-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_56-naivegw

No motifs with negative importance