112_ILC3_AbxGRMFree_A

In [1]:

# Parameters
sample_name = "ILC3_AbxGRMFree;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_112-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_112-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 20:51:30,130 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	ILC3_AbxGermFree
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	129986	103738	13.5265	23566898	3953903	0.1679	3074458	0.1306	8341960	0.3542
rep2	129986	103738	16.3446	22661367	10099210	0.446	5829083	0.2574	9620935	0.4249

Modelling Metadata

Metric	Value
auPRC	0.5876
Calibrated Recall at 50% FDR	0.207
Number of Positive Examples in Test Data	116871
Number of Negative Examples in Test Data	7953980
Imbalance Ratio in Test Data	0.0145
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
Rorc
Mbtps2

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Erg		absent
Sp3		absent
Rfx8		absent
Runx1		absent
Fos		absent
Ctcfl		absent
Nfia		absent
Klf16		absent
Rfx2		absent
Irf1		absent
Tcfeb		absent
Foxi1		absent
Nfkb1		absent
Smarcc2		absent
9430076C15Rik		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Prdm1	absent
Nfkb2	absent
Etv5	absent
Smarcc1	absent
Zfp143	absent
Sp2	absent
Pbx3	absent
Atf6	absent
Runx2	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_112-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_112-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_112-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_1, # patterns: 21, # seqlets: 25772, Positive for: ILC3_AbxGRMFree;A;GEO

pattern_0: # seqlets: 5156
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 4708
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Erg , Ets1 , Erf , Gabpa , Etv5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 2396
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Sp5 , Klf16 , Klf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1540
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Runx1 , Runx2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1391
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfkb1 , Relb , Rel , Rela , Hivep1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1307
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf1 , Prdm1 , Bcl11a , Stat2 , Irf2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 1215
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rorc , Nr1d1 , Pparg , Rora
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 1135
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Smarcc1 , Jund , Fosb , Nfe2l2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 991
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxi1 , Pbx3 , Nfya , Ybx1 , Dux
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 946
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
9430076C15Rik , Creb3 , Atf7 , Atf2 , Jdp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 738
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 680
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Erg , Ets1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 614
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Zfp143 , Tbx2 , Six5 , Zfp523
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 590
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Sp3 , Yy1 , Wt1 , Zbtb7a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 576
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcfl , Sp3 , Wt1 , Tcfap2d , Zic4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 501
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Klf16 , Klf14 , Sp8 , Sp5 , Klf7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 325
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx2 , Rfx1 , Arid2 , Rfx4 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 298
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfia , Nfix , Nfib , Nfic
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 251
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfeb , Bach2 , Mitf , Sp3 , Tcfec
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 232
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx8 , Rfx3 , Rfx5 , Rfx7 , Rfx4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 182
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_112-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_112-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_112-naivegw
Displaying motifs which has negative importances for the cell type

metacluster_0, # patterns: 20, # seqlets: 5966, Negative for: ILC3_AbxGRMFree;A;GEO

pattern_0: # seqlets: 1152
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zbtb7b , Glis1 , Zbtb7a , Glis2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 972
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zeb1 , Snai2 , Id4 , Mesp2 , Twist1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 700
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 696
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hmg20b , Onecut1 , Ahctf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 493
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ppara , Nr4a1 , Nr1h2 , Esrrg , Nr4a3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 335
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Runx1 , Runx2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 329
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Dbx1 , Tlx2 , Hmg20b , Arid3b , Pit1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 263
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Zbtb7a , E2f1 , Zfx , Wt1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 160
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tlx2 , Dbx1 , Arid3b , Ahctf1 , Hmg20b
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 139
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pitx2 , AC189028.1 , Nr5a2 , Pitx3 , Obox5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 124
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc1 , Fos , Batf , Nfe2l2 , Nfe2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 114
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 101
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hoxc9 , Hoxa9 , Cdx4 , Hoxb1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 85
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 74
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Arid3b
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 65
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pitx2 , AC189028.1 , Pitx3 , Obox5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 61
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Dbx1 , Arid3b , Tlx2 , Dmrta2 , Hmg20b
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 36
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Bcl6 , Sp3 , Maz
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 34
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 33
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1 , Zfp143
Sequence
Contrib Scores
Hyp_Contrib Scores