170_NPC_F129_A

In [1]:

# Parameters
sample_name = "NPC;F129;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_170-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_170-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 23:50:55,149 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	neural progenitor cells(F129)
Cell Group	Neural Cells and Tissues
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	217385	164371	6.7583	162522039	NA	NA	NA	NA	NA	NA

Modelling Metadata

Metric	Value
auPRC	0.587
Calibrated Recall at 50% FDR	0.293
Number of Positive Examples in Test Data	101347
Number of Negative Examples in Test Data	7969504
Imbalance Ratio in Test Data	0.0126
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
Sox3
Nfia
Rfx1
Ctcf
Ascl2

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Fos		absent
Rfx8		absent
Mef2a		absent
Mbtps2		absent
Tbpl2		absent
Creb3		absent
Foxi1		absent
Snai2		absent
Erf		absent
Smarcc2		absent
Sp3		absent
Pou2f3		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Sp2	absent
Zfp143	absent
Etv2	absent
Zfx	absent
E4f1	absent
Nfic	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_170-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_170-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_170-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_1, # patterns: 24, # seqlets: 19307, Positive for: NPC;F129;A;GEO

pattern_0: # seqlets: 3547
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 3016
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp5 , Klf16 , Klf5 , Sp1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1778
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfia , Nfix , Nfib , Nfic
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1533
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Erf , Erg , Etv5 , Gabpa , Ets1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1151
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sox3 , Sox17 , Sox6 , Sox4 , Sox9
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1068
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ascl2 , Atoh1 , Myog , Myod1 , Tcf12
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 1012
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 940
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Rfx2 , Arid2 , Rfx4 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 695
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , E2f1 , Ctcfl , Wt1 , Zfx
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 686
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Creb3 , 9430076C15Rik , Atf7 , Jdp2 , Batf3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 681
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxi1 , Pbx3 , Nfya , Ybx1 , Dux
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 585
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Ctcfl , Zfx , Tcfap2d , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 561
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Sp3 , Yy1 , Wt1 , Zfx
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 446
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 330
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx8 , Rfx5 , Rfx3 , Rfx7 , Rfx4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 273
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Tcfeb , Bach2 , Tcfec , Mitf
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 248
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pou2f3 , Pou5f1 , Tbpl2 , Evx2 , Sox2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 191
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Smarcc1 , Fosb , Jund , Nfe2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 147
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , E2f1 , Zbtb7a , Sp2 , Wt1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 145
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mef2a , Mef2c , Mef2d , Mef2b
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 95
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tbpl2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_21: # seqlets: 74
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_22: # seqlets: 64
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_23: # seqlets: 41
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Snai2 , Klf15 , Tcf4
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_170-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_170-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_170-naivegw
Displaying motifs which has negative importances for the cell type

metacluster_0, # patterns: 26, # seqlets: 10815, Negative for: NPC;F129;A;GEO

pattern_0: # seqlets: 2087
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Snai2 , Zeb1 , Id4 , Mesp2 , Twist1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 1195
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hmg20b , Arid3b
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1083
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zbtb7b , Zfp740
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1000
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 885
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sox17 , Sox9 , Sox6
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 823
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 824
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ppara , Nr4a1 , Esrrg , Nr4a3 , Nr1h2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 390
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcf15 , Tcfap4 , Tcf21 , Atoh1 , Msc
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 343
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tbp , Arid3b , Hmg20b , Tlx2 , Phf21a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 324
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfic
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 263
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hmg20b , Arid3b , Dbx1 , Tbp , Phf21a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 187
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Twist2 , Neurog3 , Bhlhe22 , Bhlhe23 , Neurod2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 170
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Klf1 , Klf3 , Klf4 , Klf2 , Klf8
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 170
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Bcl6 , Maz
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 167
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 140
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gata2 , Gata4 , Gata1 , Gata6 , Gata5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 145
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 113
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfe2l2 , Nfe2 , Fos , Jund , Batf
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 95
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Bcl6 , Maz , Sp3 , Sfpi1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 89
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2 , Nr6a1 , Esrrb , Nr5a1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 58
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Phf21a , Pou3f4 , Onecut3 , Hmg20b , Lhx3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_21: # seqlets: 49
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2 , Esrrb , Nr5a1 , Nr6a1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_22: # seqlets: 47
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_23: # seqlets: 45
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Maz , Zfp148 , Zfp281 , Bcl6
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_24: # seqlets: 62
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_25: # seqlets: 61
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1 , Zfp143 , Myc
Sequence
Contrib Scores
Hyp_Contrib Scores