226_LVR_P0_D

In [1]:

# Parameters
sample_name = "LVR;P0;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_226-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_226-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 02:45:24,367 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	liver(P0)
Cell Group	Other Tissues
Experiment Name	DHS
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	135095	84259	6.4269	132422169	11591521	0.0875	8397178	0.0634	45749468	0.3455

Modelling Metadata

Metric	Value
auPRC	0.5073
Calibrated Recall at 50% FDR	0.262
Number of Positive Examples in Test Data	41708
Number of Negative Examples in Test Data	8029143
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
Ctcf
Mbtps2
Gata6

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Jdp2		absent
Etv6		absent
Nfia		absent
Rfx1		absent
Foxa2		absent
Cebpb		absent
Hnf4g		absent
Smarcc2		absent
Fos		absent
Tbpl2		absent
Foxi1		absent
Hsf1		absent
Sp3		absent
Tcfec		absent
Rest		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Cebpg	absent
Klf2	absent
Zfp143	absent
Gm4881	absent
Pbx3	absent
Foxo1	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_226-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_226-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_226-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_1, # patterns: 21, # seqlets: 24414, Positive for: LVR;P0;D;En

pattern_0: # seqlets: 5545
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 4498
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp5 , Klf16 , Sp2 , Klf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 3237
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Etv6 , Ets1 , Sfpi1 , Elk1 , Fli1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1736
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxi1 , Pbx3 , Nfya , Ybx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1609
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1427
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Cebpb , Cebpa , Cebpd , Cebpg , Cebpe
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 832
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Zfp143 , Tbx2 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 812
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gata6 , Gata5 , Gata4 , Gata1 , Gata2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 722
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Jdp2 , Atf7 , Atf2 , Creb3 , Creb1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 715
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Yy1 , Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 683
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hnf4g , Nr1h2 , Pparg , Ppard , Nr4a3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 484
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 408
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfec , Tcfeb , Bach2 , Srebf1 , Mitf
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 406
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfia , Nfix , Nfib , Nfic
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 282
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxa2 , Foxa1 , Foxf2 , Foxc1 , Foxb1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 252
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Rfx2 , Arid2 , Rfx4 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 252
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Smarcc1 , Nfe2 , Fosb , Bach1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 247
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 172
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tbpl2 , Foxb1 , Foxc1 , Foxc2 , Foxa3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 49
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 46
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rest
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_226-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_226-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_226-naivegw
Displaying motifs which has negative importances for the cell type

metacluster_0, # patterns: 18, # seqlets: 9134, Negative for: LVR;P0;D;En

pattern_0: # seqlets: 1774
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Glis2 , Zbtb7a , Zbtb7b
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 1721
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1306
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zeb1 , Snai2 , Mga , Tcf4 , Tbx4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 707
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gata6 , Gata2 , Gata5 , Gata3 , Gata4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 552
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 534
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hnf4g , Nr1h2 , Pparg , Ppard , Nr4a3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 458
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 437
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxa3 , Foxf2 , Foxn3 , Foxc2 , Foxc1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 405
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ascl2 , Bhlha15 , Atoh1 , Myog , Msc
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 374
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Cebpb , Cebpa , Cebpd , Cebpg , Cebpe
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 374
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sox9 , Sox17 , Sox6
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 113
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pitx2 , AC189028.1 , Pitx3 , Obox5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 111
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Klf1 , Klf3 , Klf4 , Klf2 , Klf8
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 86
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Smarcc1 , Jund , Fosb , Nfe2l2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 61
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 45
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 44
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 32
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores