22_NTRPHL_A

In [1]:

# Parameters
sample_name = "NTRPHL;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_22-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_22-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 16:12:28,098 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	neutrophils
Cell Group	Other Immune Cells
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	65216	45787	10.5329	56446758	6500567	0.1152	5874698	0.1041	17967566	0.3184

Modelling Metadata

Metric	Value
auPRC	0.6356
Calibrated Recall at 50% FDR	0.202
Number of Positive Examples in Test Data	53794
Number of Negative Examples in Test Data	8017057
Imbalance Ratio in Test Data	0.0067
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

Common Motifs

Motif Name	Modisco	Homer
Creb3
Ctcf
Pbx3

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Tbpl2		absent
Tcfec		absent
Nfib		absent
Sp3		absent
Mbtps2		absent
Nfe2		absent
Relb		absent
Smarcc2		absent
Hsf1		absent
Cebpb		absent
Rfx1		absent
Irf1		absent
Sfpi1		absent
Gabpa		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Yy1	absent
Zfp143	absent
Elk1	absent
Sp5	absent
Jun	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_22-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_22-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_22-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_1, # patterns: 21, # seqlets: 24373, Positive for: NTRPHL;A;CL

pattern_0: # seqlets: 6619
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sfpi1 , Ets1 , Bcl11a , Spic , Etv6
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 3788
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp5 , Sp2 , Klf16 , Klf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1886
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1529
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Creb3 , Jdp2 , 9430076C15Rik , Atf7 , Batf3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1501
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Cebpb , Cebpd , Cebpa , Cebpg , Cebpe
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1483
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 1388
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfe2 , Nfe2l2 , Smarcc1 , Fos , Bach1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 1335
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1 , Dux
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 924
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Sp3 , Yy1 , Wt1 , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 680
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 658
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfec , Tcfeb , Bach2 , Srebf1 , Mitf
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 560
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gabpa , Fev , Erf , Erg , ENSMUSG00000044690
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 511
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf1 , Prdm1 , Bcl11a , Stat2 , Irf2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 510
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sfpi1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 229
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Rfx2 , Arid2 , Rfx4 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 212
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 204
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Relb , Nfkb1 , Rela , Hivep1 , Rel
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 161
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 110
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tbpl2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 55
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 30
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfib , Nfia , 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_22-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_22-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_22-naivegw
Displaying motifs which has negative importances for the cell type

metacluster_0, # patterns: 19, # seqlets: 8143, Negative for: NTRPHL;A;CL

pattern_0: # seqlets: 1452
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zeb1 , Snai2 , Id4 , Mesp2 , Scrt2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 1093
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Glis2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1057
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1040
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zbtb7a , Zbtb7b , Rreb1 , Klf16 , Klf6
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 827
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 409
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gli1 , Gli2 , Gli3 , Zbtb7b
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 361
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 348
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tal1 , Tcf15 , Msc , Tcf21 , Atoh8
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 286
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Cebpb , Cebpa , Cebpd , Cebpg , Cebpe
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 264
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfe2 , Nfe2l2 , Jund , Fos , Batf
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 250
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr6a1 , Esrrg , Nr5a1 , Nr5a2 , Esrrb
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 196
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pitx2 , AC189028.1 , Pitx3 , Obox5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 156
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Erg , Sfpi1 , Ets1 , ENSMUSG00000044690 , Elf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 129
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , E2f1 , Ctcfl , Zbtb7a , Sp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 66
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 62
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2 , Pitx2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 56
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 46
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 45
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2
Sequence
Contrib Scores
Hyp_Contrib Scores