182_Melanotrope_A

In [1]:

# Parameters
sample_name = "Melanotrope;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_182-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_182-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 00:33:36,612 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	FACS-purified melanotrope cells
Cell Group	Neural Cells and 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	258113	203957	7.7178	80478162	16118072	0.2003	8471919	0.1053	30573594	0.38
rep2	258113	203957	6.4851	100166213	12333774	0.1232	7545732	0.0753	34241602	0.3419

Modelling Metadata

Metric	Value
auPRC	0.5756
Calibrated Recall at 50% FDR	0.231
Number of Positive Examples in Test Data	167096
Number of Negative Examples in Test Data	7903755
Imbalance Ratio in Test Data	0.0207
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
Fos
Rfx1

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Nr4a2		absent
Nfia		absent
Mef2c		absent
Sp3		absent
Gabpa		absent
Pbx3		absent
Nfatc2		absent
Gbx1		absent
Bach2		absent
Mbtps2		absent
Fev		absent
Stat2		absent
Jdp2		absent
Smarcc2		absent
Ascl2		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Sp2	absent
Zfp143	absent
Vsx2	absent
E4f1	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_182-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_182-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_182-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_0, # patterns: 23, # seqlets: 18575, Positive for: Melanotrope;A;GEO

pattern_0: # seqlets: 2410
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 2238
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Sp5 , Klf16 , Klf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1671
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1542
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gabpa , Erf , Nr2c2 , Etv5 , Elk3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1502
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfia , Nfix , Nfib , Nfic
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1199
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gbx1 , Vsx2 , Phox2a , Phox2b , Prrx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 1086
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Smarcc1 , Jund , Fosb , Nfe2l2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 965
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Jdp2 , Creb1 , Atf2 , Atf7 , 9430076C15Rik
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 965
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ascl2 , Myod1 , Myog , Tcf12 , Id4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 942
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Rfx2 , Arid2 , Rfx4 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 595
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Stat2 , Irf1 , Irf2 , Prdm1 , Irf4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 562
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Bach2 , Tcfeb , Arntl , Pax2 , Usf2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 440
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 408
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr4a2 , Nr1d1 , Rorc , Nr4a1 , Ppara
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 405
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Sp3 , Yy1 , Wt1 , Zfx
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 399
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 301
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 282
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 202
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fev , Stat4 , Erg , Elf3 , Ets1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 157
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 158
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mef2c , Mef2a , Mef2d , Mef2b
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_21: # seqlets: 102
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfatc2 , Nfat5 , Nfatc3 , Nfatc1 , Nfatc4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_22: # seqlets: 44
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
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_182-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_182-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_182-naivegw

No motifs with negative importance