21_ESNPHL_SPLND_BlbCA

In [1]:

# Parameters
sample_name = "ESNPHL_SPLND_BlbCA;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_21-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_21-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 16:09:41,941 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	eosinophils (isolated from spleens, BalbC)
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	59033	35812	11.6043	2890857	70741	0.0246	202703	0.0705	872867	0.3036
rep2	59033	35812	17.1991	18133477	1602501	0.0885	1763619	0.0974	5291480	0.2921
rep3	59033	35812	10.7493	22921120	1258052	0.0549	1825268	0.0797	7080664	0.3092

Modelling Metadata

Metric	Value
auPRC	0.6563
Calibrated Recall at 50% FDR	0.208
Number of Positive Examples in Test Data	40644
Number of Negative Examples in Test Data	8030207
Imbalance Ratio in Test Data	0.005
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
Ctcf
Pbx3

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Gata2		absent
Smarcc2		absent
Mbtps2		absent
Gabpa		absent
Nfe2l2		absent
Irf1		absent
Sp3		absent
Rfx1		absent
Sfpi1		absent
Tbpl2		absent
Cebpb		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Klf5	absent
Elk1	absent
Zfp143	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_21-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_21-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_21-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_0, # patterns: 17, # seqlets: 22968, Positive for: ESNPHL_SPLND_BlbCA;CL

pattern_0: # seqlets: 6111
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sfpi1 , Spic , Etv6 , Spib , Ets1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 3732
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Sp5 , Klf16 , Klf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 3620
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 2219
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1 , Dux
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1561
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1304
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Creb3 , Jdp2 , Atf6 , Atf7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 1008
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Zfp143 , Tbx2 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 996
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Sp3 , Yy1 , Wt1 , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 407
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Cebpb , Cebpd , Cebpa , Cebpg , Cebpe
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 387
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfe2l2 , Nfe2 , Fos , Bach1 , Smarcc1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 328
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf1 , Prdm1 , Bcl11a , Stat2 , Irf4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 321
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gabpa , Erf , Etv5 , Erg , Fev
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 319
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sfpi1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 250
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 215
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Rfx2 , Arid2 , Rfx4 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 141
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gata2 , Gata1 , Gata6 , Gata4 , Gata5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 49
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tbpl2
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_21-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_21-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_21-naivegw

No motifs with negative importance