67_BRN_OLFTRY_BLB_A

In [1]:

# Parameters
sample_name = "BRN;OLFTRY_BLB;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_67-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_67-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 18:30:11,557 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	Brain- Olfactory Bulb
Cell Group	Neural Cells and 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	96105	54376	9.2452	50055506	4473038	0.0894	4354635	0.087	17778407	0.3553

Modelling Metadata

Metric	Value
auPRC	0.6265
Calibrated Recall at 50% FDR	0.227
Number of Positive Examples in Test Data	63502
Number of Negative Examples in Test Data	8007349
Imbalance Ratio in Test Data	0.0079
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
Gabpa
Ctcf
Rfx1
Fos

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Ascl2		absent
Pbx3		absent
Nfia		absent
Tcfap2d		absent
9430076C15Rik		absent
Mbtps2		absent
Hsf1		absent
Sox3		absent
Tcfeb		absent
Smarcc2		absent
Mef2c		absent
Irf4		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
E4f1	absent
Wt1	absent
En1	absent
Maz	absent
Mef2d	absent
Nhlh1	absent
Zfp143	absent
Hes7	absent
Tcfap2c	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_67-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_67-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_67-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_0, # patterns: 20, # seqlets: 20560, Positive for: BRN;OLFTRY_BLB;A;CL

pattern_0: # seqlets: 2991
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Wt1 , Sp5 , Klf16
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 1807
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1519
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1505
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1380
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gabpa , Erf , Ets2 , Erg , Etv5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1347
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Arid2 , Rfx2 , Rfx4 , Rfx5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 1329
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Jund , Fosb , Smarcc1 , Junb
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 1277
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 1257
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mef2c , Mef2a , Mef2d , Mef2b
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 1151
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
9430076C15Rik , Creb3 , Atf7 , Atf2 , Jdp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 934
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfia , Nfib , Nfix , Nfic
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 879
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfap2d , E2f1 , Sp3 , Wt1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 868
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Yy1 , Sp3 , Wt1 , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 655
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ascl2 , Myog , Tcf3 , Myod1 , Tcf12
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 614
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfeb , Bach2 , Tcfec , Srebf1 , Mitf
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 565
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Zfp143 , Tbx2 , Six5 , Zfp523
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 154
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 153
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sox3 , Sox6 , Sox17 , Sox9 , Sox4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 116
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf4 , Irf5 , Stat2 , Irf1 , Irf6
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 59
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_67-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_67-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_67-naivegw

No motifs with negative importance