243_wES_MSDRM_E11.5_D

In [1]:

# Parameters
sample_name = "wES;MSDRM;E11.5;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_243-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_243-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 03:31:31,637 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	Mesoderm(E11.5)
Cell Group	ES cells and embryonic tissues
Experiment Name	DHS
Experiment Group	ENCODE

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	223065	135205	12.641	79596446	15841763	0.1991	9747881	0.1225	34199054	0.4298
rep2	223065	135205	21.8567	38391254	9365640	0.2441	5845734	0.1523	17656752	0.4601

Modelling Metadata

Metric	Value
auPRC	0.6581
Calibrated Recall at 50% FDR	0.193
Number of Positive Examples in Test Data	147593
Number of Negative Examples in Test Data	7923258
Imbalance Ratio in Test Data	0.0183
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
Nr1h2
Ctcf
Pbx3
Ebf1
Rest

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Hoxa5		absent
Nfia		absent
Smarcc2		absent
Foxp4		absent
Erf		absent
Zfp281		absent
Sox3		absent
Tcf21		absent
Rfx1		absent
Hoxa9		absent
Creb3		absent
Sp3		absent
Mbtps2		absent
Tcfec		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Sp2	absent
Hoxc9	absent
Zfp143	absent
Atoh1	absent
E4f1	absent
Pknox1	absent
Rfx2	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_243-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_243-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_243-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_0, # patterns: 23, # seqlets: 21056, Positive for: wES;MSDRM;E11.5;D;En

pattern_0: # seqlets: 2909
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hoxa9 , Hoxc9 , Pbx2 , Hoxb1 , Cdx4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 2582
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcf21 , Tal1 , Msc , Ascl2 , Olig1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 2146
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1595
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sox3 , Sox17 , Sox6 , Sox9 , Sox4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1321
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Klf16 , Sp5 , Sp8
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 995
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hoxa5 , Hoxa4 , Hoxa3 , Hoxb3 , Hoxc5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 977
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 927
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 918
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ebf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 903
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zfp281 , Zfp148 , Maz , Sp2 , Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 802
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Erf , Erg , Ets1 , Etv5 , Gabpa
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 758
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr1h2 , Ppara , Hnf4g , Rxra , Pparg
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 743
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Rfx2 , Arid2 , Rfx4 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 675
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 640
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 602
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 402
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfec , Tcfeb , Bach2 , Mitf , Srebf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 397
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Creb3 , 9430076C15Rik , Atf7 , Atf2 , Batf3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 238
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfia , Nfix , Nfib , Nfic
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 176
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxp4 , Foxj3 , Gm5294 , Foxc2 , Foxj2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 175
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_21: # seqlets: 93
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Yy1 , Sp3 , Wt1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_22: # seqlets: 82
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rest
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_243-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_243-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_243-naivegw

No motifs with negative importance