278_3T3-L1_D

In [1]:

# Parameters
sample_name = "3T3-L1;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_278-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_278-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 11:30:48,871 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	3T3-L1
Cell Group	Cancer or Immortalized cells
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	218252	172233	12.4829	27634745	6283522	0.2275	3319961	0.1202	12010843	0.4349
rep2	218252	172233	4.9727	231392363	44355100	0.1917	16988140	0.0734	91212806	0.3942

Modelling Metadata

Metric	Value
auPRC	0.575
Calibrated Recall at 50% FDR	0.204
Number of Positive Examples in Test Data	152449
Number of Negative Examples in Test Data	7918402
Imbalance Ratio in Test Data	0.0189
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
Rest
Fos
Pbx3
Ctcf
Sp3
Rela
Mbtps2

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Runx1		absent
Creb3		absent
Cebpb		absent
Mef2d		absent
Smarcc2		absent
Irf1		absent
Erf		absent
Bhlha15		absent
Rfx1		absent
Hsf1		absent
Rel		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Tcf21	absent
Runx2	absent
Jdp2	absent
Zfp143	absent
Gabpa	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_278-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_278-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_278-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_1, # patterns: 24, # seqlets: 24283, Positive for: 3T3-L1;D;En

pattern_0: # seqlets: 5533
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 4504
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Smarcc1 , Jund , Fosb , Fosl1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 2482
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp5 , Klf16 , Sp2 , Klf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 2127
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfia , Nfix , Nfib , Nfic
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1784
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Erf , Etv5 , Gabpa , Erg , Elk3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1194
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 1091
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 711
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Creb3 , 9430076C15Rik , Batf3 , Atf7 , Atf2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 696
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 597
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Cebpb , Cebpd , Cebpa , Jdp2 , Cebpg
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 553
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Runx1 , Runx2 , Runx3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 532
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 488
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Bhlha15 , Tcf21 , Msc , Olig2 , Neurog1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 356
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Yy1 , Sp3 , Wt1 , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 319
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Rfx2 , Arid2 , Rfx4 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 276
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 266
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf1 , Prdm1 , Stat2 , Bcl11a , Irf2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 218
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 155
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rel , Rela , Nfkb1 , Relb , Hivep1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 113
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rest
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 106
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Tcfeb , Bach2 , Tcfec , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_21: # seqlets: 75
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_22: # seqlets: 70
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mef2d , Mef2b , Mef2c , Mef2a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_23: # seqlets: 37
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rela , Rel , Nfkb1 , Hivep1 , Nfkb2
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_278-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_278-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_278-naivegw
Displaying motifs which has negative importances for the cell type

metacluster_0, # patterns: 30, # seqlets: 11270, Negative for: 3T3-L1;D;En

pattern_0: # seqlets: 1801
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zeb1 , Snai2 , Id4 , Mesp2 , Twist1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 1535
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Glis2 , Glis1 , Zbtb7b , Gli2 , Gli1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1429
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Dbx1 , Esx1 , Tlx2 , Lhx5 , Otp
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 914
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Onecut1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 850
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ppara , Nr1h2 , Esrra , Esrrg , Nr4a1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 598
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hmg20b , Arid3b , Pit1 , Dbx1 , Onecut1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 464
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 438
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfe2l2 , Batf , Nfe2 , Jund , Fos
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 346
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sfpi1 , Spib , Ets1 , Spic , Bcl11a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 276
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 262
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 244
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx2 , Arid2 , Rfx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 241
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 198
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Arid3b , Dbx1 , Hmg20b , Lhx3 , Tlx2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 195
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Phf21a , Arid3b , Tlx2 , Hmg20b , Dbx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 182
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 168
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfic , Nfib , Nfix
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 147
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 143
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 137
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2 , Pitx2 , AC189028.1 , Pitx3 , Obox5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 136
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pitx2 , AC189028.1 , Pitx3 , Obox5 , Otx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_21: # seqlets: 91
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Klf1 , Klf14 , Klf4 , Sp8 , Klf8
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_22: # seqlets: 95
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1 , Zfp143 , Myc
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_23: # seqlets: 66
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hmg20b
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_24: # seqlets: 64
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_25: # seqlets: 62
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ebf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_26: # seqlets: 60
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Runx1 , Runx2 , Runx3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_27: # seqlets: 52
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Arid3b , Pit1 , Dbx1 , Hmg20b , Tbp
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_28: # seqlets: 35
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Yy1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_29: # seqlets: 41
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1
Sequence
Contrib Scores
Hyp_Contrib Scores