236_CRBLM_D

In [1]:

# Parameters
sample_name = "CRBLM;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_236-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_236-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 03:14:34,789 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	Cerebellum
Cell Group	Neural Cells and Tissues
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	118743	79431	14.6458	18866499	3586022	0.1902	2136418	0.1133	7588285	0.4024
rep2	118743	79431	13.2157	18243263	2968818	0.1628	1914079	0.105	6959356	0.3817
rep3	118743	79431	17.5272	28254615	7244862	0.2565	3821190	0.1353	11675589	0.4134

Modelling Metadata

Metric	Value
auPRC	0.4973
Calibrated Recall at 50% FDR	0.265
Number of Positive Examples in Test Data	103311
Number of Negative Examples in Test Data	7967540
Imbalance Ratio in Test Data	0.0128
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
Rfx1
Atoh1
Mef2d

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Sp3		absent
Fos		absent
Nfia		absent
Hlf		absent
9430076C15Rik		absent
Pbx3		absent
Rorc		absent
Erf		absent
Smarcc2		absent
Mbtps2		absent
Rfx8		absent
Zic4		absent
Hsf1		absent
Tcfeb		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Creb1	absent
Zfp143	absent
Gabpa	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_236-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_236-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_236-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_1, # patterns: 20, # seqlets: 20612, Positive for: CRBLM;D;En

pattern_0: # seqlets: 5074
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 2976
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Atoh1 , Neurod2 , Neurod1 , Msc , Tal1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 2917
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfia , Nfix , Nfib , Nfic
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1719
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Sp5 , Klf16 , Klf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1342
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1294
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 973
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
9430076C15Rik , Creb3 , Atf7 , Atf2 , Creb1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 875
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Erf , Elk3 , Ets1 , Etv4 , Etv1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 522
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hlf , Dbp , Tef , Cebpb , Nfil3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 515
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 472
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfeb , Bach2 , Tcfec , Mitf , Tcfe3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 458
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mef2d , Mef2b , Mef2c , Mef2a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 330
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Rfx2 , Arid2 , Rfx4 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 318
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Yy1 , Sp3 , Wt1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 196
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rorc , Rora , Nr1d1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 167
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zic4 , Zic3 , Zic1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 145
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Smarcc1 , Fosb , Jund , Nfe2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 140
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 101
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 78
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx8 , Rfx3 , Rfx5 , Rfx7
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_236-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_236-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_236-naivegw
Displaying motifs which has negative importances for the cell type

metacluster_0, # patterns: 25, # seqlets: 14004, Negative for: CRBLM;D;En

pattern_0: # seqlets: 2589
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , E2f1 , Sp2 , Zbtb7a , Maz
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 2295
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zfp238 , Tcf21 , Tcf15 , Bhlha15 , Msc
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1430
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Myt1l
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1327
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zeb1 , Snai2 , Mga , Tcf4 , Tbx4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 959
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfic
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 732
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hic2 , Zbtb7c , Gli3 , Gli1 , Gli2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 687
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Onecut3 , Cux2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 598
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr1h2 , Ppara , Hnf4g , Nr5a2 , Nr1i3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 546
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2 , Esrrb , Nr6a1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 395
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 392
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 363
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hmg20b , Onecut1 , Arid3b , Onecut3 , Ahctf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 353
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pitx2 , AC189028.1 , Pitx3 , Obox5 , Otx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 259
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Klf1 , Klf2 , Klf4 , Klf8 , Klf12
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 234
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 127
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Arid3b , Onecut1 , Tbp , Hmg20b , Dbx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 125
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zfp637 , Tbp , Hmg20b
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 101
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 95
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Bcl6 , Sfpi1 , Maz , Spib
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 93
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 71
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Arid3b , Dbx1 , Onecut1 , Tbp , Tlx2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_21: # seqlets: 69
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_22: # seqlets: 68
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Bcl6 , Sfpi1 , Irf1 , Spib , Bcl11a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_23: # seqlets: 58
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Bcl6
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_24: # seqlets: 38
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rreb1
Sequence
Contrib Scores
Hyp_Contrib Scores