228_LNG_P0_D

In [1]:

# Parameters
sample_name = "LNG;P0;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_228-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_228-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 02:51:17,479 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	lung(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	246689	169517	8.101	143292993	28138253	0.1964	12705809	0.0887	58149700	0.4059
rep2	246689	169517	9.1026	96062636	15477824	0.1612	8565561	0.0892	37645170	0.392

Modelling Metadata

Metric	Value
auPRC	0.5922
Calibrated Recall at 50% FDR	0.23
Number of Positive Examples in Test Data	153827
Number of Negative Examples in Test Data	7917024
Imbalance Ratio in Test Data	0.0191
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
Nfia
Mbtps2
Rest
Pbx3
Ctcf

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Atf2		absent
Nkx2-6		absent
Tcf21		absent
Grhl1		absent
Mef2a		absent
Sp3		absent
Cebpb		absent
Fos		absent
Foxc2		absent
Ets1		absent
Irf1		absent
Smarcc2		absent
Tcfec		absent
Rfx1		absent
Klf5		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Tcfcp2	absent
Cebpd	absent
Ferd3l	absent
Nfic	absent
Zfp143	absent
Sp2	absent
Foxb1	absent
Creb3	absent
Smarcc1	absent
Mef2b	absent
Etv4	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_228-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_228-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_228-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_1, # patterns: 23, # seqlets: 23010, Positive for: LNG;P0;D;En

pattern_0: # seqlets: 3444
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 2866
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ets1 , Erg , Erf , Etv5 , Etv6
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 2433
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Klf5 , Klf16 , Sp3 , Klf2 , Sp5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1942
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfia , Nfib , Nfix , Nfic
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1921
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Cebpb , Cebpa , Cebpd , Cebpg , Cebpe
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1452
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Atf2 , Atf7 , 9430076C15Rik , Creb3 , Jdp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 1000
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxc2 , Foxc1 , Foxb1 , Foxd1 , Foxf2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 924
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 864
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Sp5 , Klf16 , Klf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 836
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Smarcc1 , Jund , Fosb , Nfe2l2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 788
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1 , Dux
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 748
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcf21 , Figla , Ascl2 , Tcfap4 , Atoh8
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 691
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 466
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nkx2-6 , Nkx2-4 , Nkx2-9 , Nkx2-3 , Nkx2-2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 462
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfec , Tcfeb , Bach2 , Mitf , Usf2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 451
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Rfx2 , Arid2 , Rfx4 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 411
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mef2a , Mef2c , Mef2d , Mef2b
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 403
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf1 , Prdm1 , Stat2 , Irf4 , Bcl11a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 278
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 275
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Sp3 , Yy1 , Wt1 , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 232
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Grhl1 , Tcfcp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_21: # seqlets: 66
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rest
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_22: # seqlets: 57
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_228-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_228-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_228-naivegw
Displaying motifs which has negative importances for the cell type

metacluster_0, # patterns: 18, # seqlets: 10565, Negative for: LNG;P0;D;En

pattern_0: # seqlets: 2631
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Dbx1 , Pou4f1 , Arid3b , Tlx2 , Lhx5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 1984
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1498
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Snai2 , Zeb1 , Id4 , Mesp2 , Twist1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 997
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zbtb7b
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 816
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Glis2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 687
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfic , Nfia , Nfix , Hic1 , Nfib
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 580
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sox17 , Sox9 , Sox6 , Sox2 , Sox14
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 501
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Erg , Ets1 , ENSMUSG00000044690 , Elf5 , Fev
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 215
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ascl2 , Tcf3 , Figla , Atoh1 , Tcf15
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 132
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxd3 , Foxm1 , Foxa3 , Foxn3 , Foxp4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 85
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Bcl6 , Sfpi1 , Spib , Maz , Irf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 80
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Bcl6
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 74
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2 , Esrrb , Nr6a1 , Nr5a1 , Esrrg
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 65
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Bcl6 , Sfpi1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 79
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 64
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 42
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 35
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxd3 , Foxm1 , Foxj1 , Onecut2 , Foxp4
Sequence
Contrib Scores
Hyp_Contrib Scores