72_BRN_CRBLM_A

In [1]:

# Parameters
sample_name = "BRN;CRBLM;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_72-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_72-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 18:45:03,739 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	Brain- Cerebellum
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	74560	47910	10.9686	47061682	4374633	0.093	4249256	0.0903	16254682	0.3455

Modelling Metadata

Metric	Value
auPRC	0.6228
Calibrated Recall at 50% FDR	0.242
Number of Positive Examples in Test Data	57412
Number of Negative Examples in Test Data	8013439
Imbalance Ratio in Test Data	0.0071
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
Pbx3
Sp3
Ctcf
Jdp2

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Nfia		absent
Atoh1		absent
Irf1		absent
Fos		absent
Mbtps2		absent
Tcfeb		absent
Mef2b		absent
Ets1		absent
Wt1		absent
Smarcc2		absent
Rfx1		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Zfp143	absent
Klf5	absent
Maz	absent
E2f1	absent
Grhl1	absent
Nfic	absent
Yy1	absent
Tal1	absent
Gabpa	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_72-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_72-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_72-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_0, # patterns: 17, # seqlets: 18938, Positive for: BRN;CRBLM;A;CL

pattern_0: # seqlets: 2862
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Zbtb7a , Sp1 , Maz
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 2623
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 2031
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1647
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1611
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ets1 , Gabpa , Elk3 , Elk1 , Etv4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1525
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfia , Nfic , Nfix , Nfib
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 1414
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Jdp2 , Atf7 , 9430076C15Rik , Atf2 , Creb1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 1064
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Atoh1 , Neurod2 , Neurod1 , Msc , Tal1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 851
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Wt1 , Sp3 , Egr4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 687
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Sp3 , Yy1 , Wt1 , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 617
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Six5 , Zfp523
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 546
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfeb , Tcfec , Bach2 , Mitf , Tcfe3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 532
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Rfx2 , Arid2 , Rfx4 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 338
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf1 , Stat2 , Irf2 , Prdm1 , Irf4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 244
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Smarcc1 , Fosb , Nfe2 , Bach1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 232
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 114
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mef2b , Mef2c , Mef2a , Mef2d
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_72-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_72-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_72-naivegw

No motifs with negative importance