18_Mast_A

In [1]:

# Parameters
sample_name = "Mast;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_18-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_18-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 16:01:17,877 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	mast cells
Cell Group	Other Immune Cells
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	93774	56592	10.7667	57556873	4643301	0.0807	3991828	0.0694	16836341	0.2926

Modelling Metadata

Metric	Value
auPRC	0.5777
Calibrated Recall at 50% FDR	0.233
Number of Positive Examples in Test Data	58384
Number of Negative Examples in Test Data	8012467
Imbalance Ratio in Test Data	0.0072
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

Common Motifs

Motif Name	Modisco	Homer
Runx1
Pbx3
Ctcf
Mbtps2

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Nfe2l2		absent
Tcfec		absent
Ets1		absent
E2f1		absent
Hsf1		absent
Sfpi1		absent
Irf1		absent
Smarcc2		absent
Nfia		absent
9430076C15Rik		absent
Stat4		absent
Sp3		absent
Gata4		absent
Rfx1		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Elk1	absent
Zfp143	absent
Sp2	absent
E4f1	absent
Gata2	absent
Klf16	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_18-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_18-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_18-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_0, # patterns: 21, # seqlets: 20458, Positive for: Mast;A;CL

pattern_0: # seqlets: 3646
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sfpi1 , Ets1 , Etv6 , Spic , Erg
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 2581
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 2277
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Zbtb7a , Sp5 , Maz
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1863
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1 , Dux
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1455
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1118
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Runx1 , Runx2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 949
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
9430076C15Rik , Creb3 , Jdp2 , Atf7 , Creb1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 843
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gata4 , Gata2 , Gata1 , Mecom , Gata6
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 821
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfe2l2 , Nfe2 , Bach1 , Smarcc1 , Fos
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 776
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 721
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Yy1 , Sp3 , Zbtb7a , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 688
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Maz , Zbtb7a , Zfp148
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 687
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf1 , Stat2 , Prdm1 , Irf4 , Irf2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 522
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfec , Tcfeb , Bach2 , Mitf , Srebf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 357
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
E2f1 , Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 285
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Ctcfl , Zfx , E2f1 , Zbtb7a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 269
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Rfx2 , Arid2 , Rfx4 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 226
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ets1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 196
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfia , Nfix , Nfib , Nfic
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 90
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 88
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Stat4 , Stat5a , Stat1 , Stat5b , Stat6
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_18-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_18-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_18-naivegw

No motifs with negative importance