189_pMeg_A

In [1]:

# Parameters
sample_name = "pMeg;A;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_189-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_189-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 00:57:22,822 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	Megakaryocyte primary cell
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	134033	96187	17.9057	30178694	6595393	0.2187	4333984	0.1437	11749993	0.3896
rep2	134033	96187	17.7766	29885640	7123197	0.2385	4365552	0.1462	11905837	0.3986

Modelling Metadata

Metric	Value
auPRC	0.6153
Calibrated Recall at 50% FDR	0.238
Number of Positive Examples in Test Data	109130
Number of Negative Examples in Test Data	7961721
Imbalance Ratio in Test Data	0.0135
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
Sfpi1

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Hsf1		absent
Nfe2		absent
Sp3		absent
Foxi1		absent
Mbtps2		absent
Bcl11a		absent
Tcfeb		absent
Cebpb		absent
Elk1		absent
Smarcc2		absent
Fos		absent
Runx1		absent
Smarcc1		absent
Creb3		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Cebpa	absent
Pbx3	absent
Zfp143	absent
Yy1	absent
Ctcfl	absent
Srebf2	absent
Sp2	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_189-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_189-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_189-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_1, # patterns: 23, # seqlets: 27681, Positive for: pMeg;A;En

pattern_0: # seqlets: 8920
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 7530
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sfpi1 , Spib , Ets1 , Bcl11a , Spic
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 2689
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Cebpb , Cebpa , Cebpd , Cebpg , Cebpe
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 2039
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp5 , Klf16 , Klf5 , Klf14
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1582
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Bcl11a , Irf1 , Prdm1 , Sfpi1 , Zscan10
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 964
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Elk1 , Erf , Elk3 , Ets1 , Elk4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 770
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sfpi1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 581
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 400
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Creb3 , Atf7 , 9430076C15Rik , Jdp2 , Batf3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 391
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfe2 , Nfe2l2 , Bach1 , Fos , Smarcc1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 355
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 251
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxi1 , Pbx3 , Nfya , Ybx1 , Dux
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 216
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 199
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Runx1 , Runx2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 170
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Yy1 , Sp3 , Wt1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 135
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfeb , Bach2 , Mitf , Tcfec , Tcfe3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 110
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc1 , Erg , Bcl11a , Fev , Fos
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 105
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 107
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 51
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Runx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 45
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Smarcc1 , Jund , Sfpi1 , Fosb
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_21: # seqlets: 39
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_22: # seqlets: 32
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1
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_189-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_189-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_189-naivegw
Displaying motifs which has negative importances for the cell type

metacluster_0, # patterns: 24, # seqlets: 11223, Negative for: pMeg;A;En

pattern_0: # seqlets: 2140
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zbtb7b , Zfp219 , Plagl1 , Zfp202 , Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 1303
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zeb1 , Snai2 , Mga , Tcf4 , Tbx4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1270
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sfpi1 , Bcl11a , Erg , Ets1 , Etv6
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1170
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Maz , Sp3 , Zfp148 , Zfp281 , Rreb1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 949
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 911
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Cebpb , Cebpa , Cebpd , Cebpg , Cebpe
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 510
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcf15 , Tal1 , Tcf21 , Msc , Atoh1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 378
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gata4 , Gata2 , Gata1 , Mecom , Gata6
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 373
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfe2l2 , Nfe2 , Jund , Batf , Fos
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 348
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Egr2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 249
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 200
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 204
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 174
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 154
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 152
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1 , Zfp143
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 148
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 134
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pitx2 , AC189028.1 , Nr5a2 , Pitx3 , Obox5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 128
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 83
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Egr2 , Hif3a , Rreb1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 74
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a1 , Nr5a2 , Nr6a1 , Esrrb , Esrrg
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_21: # seqlets: 71
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2 , Esrrb , Nr6a1 , Nr5a1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_22: # seqlets: 51
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2 , Nr6a1 , Esrrb , Nr5a1 , Esrrg
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_23: # seqlets: 49
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2 , Esrrb , Nr6a1
Sequence
Contrib Scores
Hyp_Contrib Scores