4_NK_SPLND_A

In [1]:

# Parameters
sample_name = "NK_SPLND;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_4-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_4-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 15:19:13,027 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	NK cells (spleen)
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	97377	74703	13.1018	33564780	6500327	0.1938	5009038	0.1493	10935616	0.326
rep2	97377	74703	18.2143	21920687	6277000	0.2866	4641827	0.2119	7498029	0.3424

Modelling Metadata

Metric	Value
auPRC	0.6008
Calibrated Recall at 50% FDR	0.212
Number of Positive Examples in Test Data	87997
Number of Negative Examples in Test Data	7982854
Imbalance Ratio in Test Data	0.0109
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
T
Pbx3
Ctcf

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Rela		absent
Mef2a		absent
Erg		absent
Rfx1		absent
Tcfec		absent
Mbtps2		absent
Smarcc2		absent
Klf1		absent
Irf1		absent
9430076C15Rik		absent
Runx2		absent
Fos		absent
Ets1		absent
Nfia		absent
Sp3		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Erf	absent
Zfp143	absent
E4f1	absent
Klf5	absent
E2f1	absent
Yy1	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_4-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_4-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_4-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_0, # patterns: 21, # seqlets: 22188, Positive for: NK_SPLND;A;CL

pattern_0: # seqlets: 4688
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Erg , Ets1 , Erf , Etv5 , Etv6
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 2027
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp5 , Klf16 , Sp2 , Klf14
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1872
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1647
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Sp5 , Klf5 , Klf2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1468
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf1 , Prdm1 , Stat2 , Irf2 , Irf4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1366
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Runx2 , Runx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 1307
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1 , Dux
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 1166
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
9430076C15Rik , Creb3 , Atf7 , Atf2 , Jdp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 1031
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Wt1 , E2f1 , Zfx , Klf15
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 937
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 629
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Jund , Smarcc1 , Fosb , Nfe2l2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 610
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ets1 , Erg , Gabpa , Ets2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 598
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Yy1 , Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 575
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfec , Tcfeb , Bach2 , Mitf , Srebf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 552
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Zfp143 , Tbx2 , Six5 , Zfp523
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 539
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
T , Tbx1 , Tbx20 , Mga , Tbx15
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 369
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Rfx2 , Arid2 , Rfx4 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 264
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Klf1 , Klf2 , Klf4 , Klf8 , Klf3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 207
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rela , Relb , Nfkb1 , Rel , Hivep1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 174
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfia , Nfib , Nfix , Nfic
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 162
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mef2a , Mef2c , Mef2d , Mef2b
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_4-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_4-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_4-naivegw

No motifs with negative importance