195_DC_LPS_4h_A

In [1]:

# Parameters
sample_name = "DC_LPS;4h;A;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_195-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_195-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 01:16:06,024 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	dendritic cell(100 ng/mL Lipopolysaccharide, 4hours)
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	142641	96690	17.1295	29455074	11012580	0.3741	6221966	0.2114	12851062	0.4366
rep2	142641	96690	6.515	78975437	4579417	0.058	4334187	0.0549	26151567	0.3312

Modelling Metadata

Metric	Value
auPRC	0.6434
Calibrated Recall at 50% FDR	0.182
Number of Positive Examples in Test Data	120926
Number of Negative Examples in Test Data	7949925
Imbalance Ratio in Test Data	0.015
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
Rela
Sfpi1
Sp3
Ctcf

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Hsf1		absent
Tbpl2		absent
Elk3		absent
Creb3		absent
Nfia		absent
Smarcc2		absent
Bcl11a		absent
Fos		absent
Foxi1		absent
Tcfeb		absent
Runx1		absent
Mef2d		absent
Cebpb		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Nfe2l2	absent
Zfp143	absent
Jdp2	absent
Irf4	absent
Pbx3	absent
Yy1	absent
Grhl1	absent
Runx2	absent
Creb1	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_195-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_195-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_195-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_1, # patterns: 19, # seqlets: 23742, Positive for: DC_LPS;4h;A;En

pattern_0: # seqlets: 4745
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sfpi1 , Spib , Bcl11a , Spic , Ets1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 3226
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 2766
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp5 , Klf16 , Klf5 , Klf14
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 2175
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Bcl11a , Irf1 , Prdm1 , Stat2 , Irf4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1551
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rela , Nfkb1 , Relb , Rel , Hivep1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1482
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Cebpb , Cebpd , Cebpa , Cebpg , Cebpe
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 1434
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 1427
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Smarcc1 , Nfe2 , Nfe2l2 , Fosb
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 1104
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Creb3 , 9430076C15Rik , Batf3 , Atf7 , Atf2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 891
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Elk3 , Etv4 , Erf , Etv1 , Gm5454
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 772
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxi1 , Pbx3 , Nfya , Ybx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 622
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Runx1 , Runx2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 469
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Mbtps2 , Wt1 , Yy1 , Sp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 464
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfeb , Bach2 , Tcfec , Mitf , Tcfe3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 311
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 100
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 82
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mef2d , Mef2c , Mef2b , Mef2a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 79
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tbpl2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 42
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfia , Nfib , Nfix , Nfic
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_195-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_195-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_195-naivegw
Displaying motifs which has negative importances for the cell type

metacluster_0, # patterns: 30, # seqlets: 10405, Negative for: DC_LPS;4h;A;En

pattern_0: # seqlets: 2362
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Lhx5 , Dbx1 , Lhx1 , Tlx2 , Lhx3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 1421
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Snai2 , Zeb1 , Id4 , Atoh8 , Mesp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 959
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Glis2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 851
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 844
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 591
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ppara , Nr1h2 , Nr4a1 , Nr4a3 , Esrrb
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 403
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sfpi1 , Bcl11a , Erg , Elf5 , ENSMUSG00000044690
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 386
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zbtb7c , Gli1 , Gli2 , Gli3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 320
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Maz , Zfp281 , Zfp148 , Sp3 , Rreb1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 260
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Arid3b , Tlx2 , Dbx1 , Onecut1 , Hmg20b
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 188
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Maz , Zbtb7a , Wt1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 176
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Maz , Sp3 , Rreb1 , Zfp281 , Zfp148
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 173
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Maz , Sp3 , Zfp148 , Zfp281 , Rreb1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 172
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Arid3b , Tlx2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 159
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Zbtb7a , Sp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 160
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Nfe2l2 , Batf , Nfe2 , Jund
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 113
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Cebpd , Cebpb , Cebpg , Cebpe , Cebpa
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 99
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Klf15 , Rreb1 , Sp3 , Maz , Zfp281
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 93
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxd3 , Foxm1 , Bcl6 , Irf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 93
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 85
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Arid3b
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_21: # seqlets: 64
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rel , Hivep1 , Nfkb1 , Relb , Rela
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_22: # seqlets: 56
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_23: # seqlets: 51
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Onecut2 , Runx2 , Foxd3 , Foxm1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_24: # seqlets: 49
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_25: # seqlets: 81
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2 , Esrrb
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_26: # seqlets: 44
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rel , Rela , Relb , Hivep1 , Nfkb2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_27: # seqlets: 64
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pitx2 , AC189028.1 , Pitx3 , Obox5 , Nr5a2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_28: # seqlets: 58
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_29: # seqlets: 30
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores