186_ES_JM8.N4_Asynch_A

In [1]:

# Parameters
sample_name = "ES;JM8.N4;Asynch;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_186-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_186-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 00:47:39,916 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	JM8.N4 Asynchronous
Cell Group	ES cells and embryonic tissues
Experiment Name	ATAC
Experiment Group	GEO

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	137776	97818	4.6453	176383965	8614474	0.0488	9551189	0.0542	54514429	0.3091
rep2	137776	97818	3.533	197121315	8359286	0.0424	10010761	0.0508	63031595	0.3198

Modelling Metadata

Metric	Value
auPRC	0.7026
Calibrated Recall at 50% FDR	0.199
Number of Positive Examples in Test Data	38727
Number of Negative Examples in Test Data	8032124
Imbalance Ratio in Test Data	0.0048
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
Mbtps2
Pbx3

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Sp3		absent
Hsf1		absent
Elk3		absent
Smarcc2		absent
Smarcc1		absent
Sox2		absent
Sox3		absent
Creb3		absent
Grhl1		absent
Rest		absent
Rfx2		absent
Rfx8		absent
Tcfeb		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Gabpa	absent
Zfp143	absent
Klf7	absent
E2f7	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_186-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_186-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_186-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_0, # patterns: 21, # seqlets: 18997, Positive for: ES;JM8.N4;Asynch;A;GEO

pattern_0: # seqlets: 6213
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Klf16 , Klf5 , Sp5 , Sp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 2132
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1535
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1458
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1237
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Ctcfl , Wt1 , E2f1 , Sp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 811
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Elk3 , Elk1 , Ets1 , Erf , Elk4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 675
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sox2 , Pou5f1 , Tbpl2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 662
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Creb3 , Atf7 , Jdp2 , 9430076C15Rik , Atf2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 652
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Yy1 , Sp3 , Wt1 , Zbtb7a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 619
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Zfp143 , Tbx2 , Six5 , Zfp523
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 547
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sox3 , Sox2 , Sox9 , Sox4 , Sox6
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 514
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfeb , Bach2 , Tcfec , Mitf , Tcfe3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 407
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc1 , Bach1 , Nfe2l2 , Nfe2 , Fos
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 378
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 366
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx2 , Rfx1 , Arid2 , Rfx4 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 220
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx8 , Rfx3 , Rfx5 , Sp3 , Rfx4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 147
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 129
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 128
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 91
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Grhl1 , Tcfcp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 76
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rest , Sp3 , Wt1
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_186-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_186-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_186-naivegw

No motifs with negative importance