144_Erythroid_Ter119+_A

In [1]:

# Parameters
sample_name = "Erythroid;Ter119+;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_144-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_144-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 22:23:47,584 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	Ter119+ Erythroid cells
Cell Group	Other Immune Cells
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	45623	33619	9.5158	47165654	2269105	0.0481	2855225	0.0606	14556630	0.3088
rep2	45623	33619	9.116	51530014	2388041	0.0464	3026133	0.0587	15861839	0.3079

Modelling Metadata

Metric	Value
auPRC	0.6228
Calibrated Recall at 50% FDR	0.212
Number of Positive Examples in Test Data	36430
Number of Negative Examples in Test Data	8034421
Imbalance Ratio in Test Data	0.0045
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
Smarcc2
Pbx3
Creb3
Ctcf

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Irf1		absent
Mbtps2		absent
Nfib		absent
Tcfeb		absent
Sp3		absent
Tbpl2		absent
Klf1		absent
Nfe2		absent
Gata5		absent
Elk1		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Bach1	absent
Yy1	absent
Klf7	absent
Gata1	absent
Gabpa	absent
Zfx	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_144-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_144-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_144-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_0, # patterns: 16, # seqlets: 20910, Positive for: Erythroid;Ter119+;A;GEO

pattern_0: # seqlets: 3639
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 2874
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Sp5 , Klf5 , Klf16
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 2387
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Elk1 , Erf , Elk3 , Nr2c2 , Elk4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 2074
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1 , Dux
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1695
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Klf1 , Klf2 , Klf4 , Klf8 , Klf12
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1438
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Sp3 , Yy1 , Wt1 , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 1300
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 1142
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gata5 , Gata6 , Gata4 , Gata1 , Gata2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 1050
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Zfp143 , Tbx2 , Six5 , Zfp523
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 903
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Creb3 , Jdp2 , Atf7 , Atf2 , Creb1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 791
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfe2 , Nfe2l2 , Bach1 , Fos , Smarcc1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 561
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf1 , Prdm1 , Stat2 , Irf2 , Bcl11a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 556
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfeb , Bach2 , Sp3 , Tcfec , Arntl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 359
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 93
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfib , Nfia , Nfix , Nfic , Meis1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 48
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tbpl2 , Sox2
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_144-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_144-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_144-naivegw

No motifs with negative importance