57_Adipose_A

In [1]:

# Parameters
sample_name = "Adipose;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_57-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_57-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 17:59:48,668 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	Adipose
Cell Group	Other Tissues
Experiment Name	ATAC
Experiment Group	Casellas Lab

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	59064	36655	10.5352	18574604	1352099	0.0729	1862774	0.1004	6129555	0.3303
rep2	59064	36655	6.36	53206816	1823426	0.0343	2958154	0.0556	16743725	0.3148

Modelling Metadata

Metric	Value
auPRC	0.7077
Calibrated Recall at 50% FDR	0.163
Number of Positive Examples in Test Data	40627
Number of Negative Examples in Test Data	8030224
Imbalance Ratio in Test Data	0.005
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
Sp3
Creb3

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Irf1		absent
Klf16		absent
Mbtps2		absent
Foxi1		absent
Ets1		absent
Erg		absent
Smarcc2		absent
Fos		absent
Tcfec		absent
Rfx1		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Elk1	absent
Pbx3	absent
Zfp143	absent
Yy1	absent
Prdm1	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_57-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_57-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_57-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_1, # patterns: 16, # seqlets: 23679, Positive for: Adipose;A;CL

pattern_0: # seqlets: 4777
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Sp5 , Klf5 , Klf16
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 4738
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Erg , Ets1 , Erf , Sfpi1 , Gabpa
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 4282
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1890
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxi1 , Pbx3 , Nfya , Ybx1 , Dux
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1876
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1038
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf1 , Bcl11a , Prdm1 , Irf2 , Stat2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 950
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 868
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Yy1 , Sp3 , Wt1 , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 812
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Klf16 , Klf14 , Sp8 , Sp5 , Klf7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 720
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Creb3 , Atf7 , Jdp2 , Creb1 , 9430076C15Rik
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 567
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfec , Tcfeb , Bach2 , Mitf , Tcfe3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 392
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Rfx2 , Arid2 , Rfx4 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 304
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Smarcc1 , Jund , Fosb , Nfe2l2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 243
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 126
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ets1 , Ets2 , Erg
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 96
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_57-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_57-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_57-naivegw
Displaying motifs which has negative importances for the cell type

metacluster_0, # patterns: 22, # seqlets: 10967, Negative for: Adipose;A;CL

pattern_0: # seqlets: 2422
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Dbx1 , Tlx2 , Sebox , Nkx6-1 , Arid3b
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 1880
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zbtb7b , Glis2 , Glis1 , Zbtb7a , Zic5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1462
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Zfp148 , Wt1 , Hic2 , Zfp281
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1317
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zeb1 , Snai2 , Id4 , Mesp2 , Scrt1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 884
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcf15 , Atoh1 , Tal1 , Tcfap4 , Bhlha15
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 740
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 431
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Erg , Ets1 , Fev , ENSMUSG00000044690 , Elf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 204
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 188
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gata1 , Gata4 , Gata2 , Mecom , Gata6
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 179
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Zfx , Zbtb7a , Maz
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 171
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Tcfap2d , Ctcfl , Mbd2 , Egr4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 154
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2 , Pitx2 , AC189028.1 , Pitx3 , Obox5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 143
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 139
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2 , Hsf1 , Nr6a1 , Esrrb
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 136
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sox17 , Sox6 , Sox3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 134
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 119
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Klf5 , Klf4 , Sp5 , Klf2 , Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 67
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 69
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 53
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2 , Esrrb , Nr6a1 , Prdm4 , Nr5a1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 42
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_21: # seqlets: 33
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Esrrb , Nr6a1 , Esrrg , Nr4a1 , Nr5a1
Sequence
Contrib Scores
Hyp_Contrib Scores