58_Mammary_A

In [1]:

# Parameters
sample_name = "Mammary;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_58-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_58-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 18:02:45,077 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	Mammary tissue
Cell Group	Other Tissues
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	67951	35799	7.8519	14580227	516737	0.0355	1100752	0.0756	4879976	0.3351
rep2	67951	35799	6.7582	35160853	1476217	0.042	2423212	0.069	11746475	0.3343

Modelling Metadata

Metric	Value
auPRC	0.6427
Calibrated Recall at 50% FDR	0.189
Number of Positive Examples in Test Data	41634
Number of Negative Examples in Test Data	8029217
Imbalance Ratio in Test Data	0.0052
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

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Smarcc2		absent
Gabpa		absent
Grhl1		absent
Nfia		absent
Prdm1		absent
Foxi1		absent
Fos		absent
9430076C15Rik		absent
Sox6		absent
Ctcf		absent
Sp3		absent
Cebpb		absent
Rel		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Elk1	absent
Hes7	absent
Stat1	absent
Klf7	absent
E4f1	absent
Mbtps2	absent
Zfp143	absent
Pbx3	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_58-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_58-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_58-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_0, # patterns: 21, # seqlets: 19797, Positive for: Mammary;A;CL

pattern_0: # seqlets: 3181
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gabpa , Sp3 , Elk3 , Ets2 , Elk1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 2529
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp5 , Sp2 , Klf16 , Klf14
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1754
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Klf16 , Sp1 , Klf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1645
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1530
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxi1 , Pbx3 , Nfya , Ybx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1496
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfia , Nfix , Nfib , Nfic , Insm1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 1478
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
9430076C15Rik , Creb3 , Creb1 , Jdp2 , Atf7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 1281
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 1205
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Mbtps2 , Yy1 , Wt1 , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 790
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 720
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sox6 , Sox3 , Sox17 , Sox9 , Sox4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 504
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Cebpb , Cebpd , Cebpa , Cebpg , Cebpe
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 501
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Zfx , Tcfap2d , E2f1 , Zbtb7a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 298
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Grhl1 , Tcfcp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 224
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , E2f1 , Sp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 222
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Prdm1 , Irf4 , Stat2 , Irf1 , Irf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 194
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Smarcc1 , Jund , Fosb , Junb
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 121
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 47
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rel , Rela , Nfkb1 , Relb , Hivep1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 43
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 34
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_58-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_58-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_58-naivegw

No motifs with negative importance