192_pErythroblast_A

In [1]:

# Parameters
sample_name = "pErythroblast;A;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_192-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_192-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 01:06:35,009 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	Erythroblast primary cell
Cell Group	Other Immune Cells
Experiment Name	ATAC
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	69214	51798	10.2287	30401327	3956009	0.1302	3996138	0.1315	10401378	0.3423
rep2	69214	51798	10.7078	26706298	3463247	0.1298	3539442	0.1326	9248240	0.3465

Modelling Metadata

Metric	Value
auPRC	0.558
Calibrated Recall at 50% FDR	0.192
Number of Positive Examples in Test Data	53311
Number of Negative Examples in Test Data	8017540
Imbalance Ratio in Test Data	0.0066
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
Mbtps2
Gabpa
Sp3
Ctcf

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Nfe2		absent
Smarcc2		absent
Hsf1		absent
Foxi1		absent
Creb3		absent
Nfix		absent
Tcfeb		absent
Irf1		absent
Gata6		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Zfp143	absent
Fosl2	absent
Pbx3	absent
Nfe2l2	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_192-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_192-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_192-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_1, # patterns: 16, # seqlets: 23696, Positive for: pErythroblast;A;En

pattern_0: # seqlets: 8144
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 4262
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Sp5 , Klf5 , Klf16
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1867
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gabpa , Ets1 , Elk3 , Nr2c2 , Erf
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1842
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1488
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxi1 , Pbx3 , Nfya , Ybx1 , Dux
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1007
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Sp3 , Yy1 , Wt1 , Klf15
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 961
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Zfp143 , Tbx2 , Six5 , Zfp523
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 829
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfe2 , Nfe2l2 , Bach1 , Fos , Smarcc1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 804
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Creb3 , Jdp2 , Atf7 , Atf2 , 9430076C15Rik
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 782
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gata6 , Gata5 , Gata4 , Gata1 , Gata2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 769
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl , Thrb
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 320
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 304
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfeb , Bach2 , Tcfec , Sp3 , Mitf
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 197
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf1 , Prdm1 , Stat2 , Bcl11a , Irf2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 74
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfix , Nfib , Nfia , Nfic , Smad1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 46
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1
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_192-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_192-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_192-naivegw
Displaying motifs which has negative importances for the cell type

metacluster_0, # patterns: 24, # seqlets: 8752, Negative for: pErythroblast;A;En

pattern_0: # seqlets: 1413
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gata2 , Gata6 , Gata4 , Gata3 , Gata5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 1276
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1062
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hoxa9 , Hoxc9
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 687
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcf4 , Twist1 , Mesp2 , Snai2 , Id4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 639
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gli1 , Gli2 , Gli3 , Zbtb7b
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 475
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Klf1 , Klf2 , Klf8 , Klf4 , Klf3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 430
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcf15 , Tal1 , Msc , Neurod2 , Neurod1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 418
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 363
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 271
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 247
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Dbx1 , Tlx2 , Lhx5 , Lhx3 , Arid3b
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 239
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 219
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rela
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 143
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1 , Myc
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 139
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2 , Pitx2 , AC189028.1 , Pitx3 , Obox5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 120
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Zbtb7a , Sp2 , Maz , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 106
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hivep1 , Nfkb1 , Nfatc2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 104
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Fosb , Smarcc1 , Nfe2 , Jund
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 102
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 91
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 81
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_21: # seqlets: 45
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2 , Maz , Esrrb
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_22: # seqlets: 44
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pitx2 , AC189028.1 , Pitx3 , Obox5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_23: # seqlets: 38
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pitx2 , AC189028.1 , Pitx3 , Obox5
Sequence
Contrib Scores
Hyp_Contrib Scores