245_wES.Fr_BRN_E14.4_D

In [1]:

# Parameters
sample_name = "wES.Fr_BRN;E14.4;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_245-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_245-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 03:38:27,805 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	mixed embryonic mouse forebrain(E14.5)
Cell Group	ES cells and embryonic 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	246559	175353	9.1438	160155200	NA	NA	NA	NA	NA	NA
rep2	246559	175353	12.3608	66293262	16582997	0.2502	11073359	0.1671	28706259	0.4331

Modelling Metadata

Metric	Value
auPRC	0.7114
Calibrated Recall at 50% FDR	0.16
Number of Positive Examples in Test Data	187944
Number of Negative Examples in Test Data	7882907
Imbalance Ratio in Test Data	0.0233
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
Rfx1
Nfia
Ctcf

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Lhx2		absent
Zfp281		absent
Erf		absent
Sox3		absent
9430076C15Rik		absent
Smarcc2		absent
Tbpl2		absent
Tcfeb		absent
Sp3		absent
Atoh1		absent
Pbx3		absent
Mef2a		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Gbx1	absent
Zfp143	absent
E4f1	absent
E2f1	absent
Klf5	absent
Bhlhe22	absent
Hmga2	absent
Gabpa	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_245-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_245-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_245-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_0, # patterns: 19, # seqlets: 16448, Positive for: wES.Fr_BRN;E14.4;D;En

pattern_0: # seqlets: 2753
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 2174
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1787
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Lhx2 , Lhx9 , Pax6 , Gsx1 , Lbx2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1393
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Klf16 , Sp5 , Sp2 , Klf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1256
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Atoh1 , Neurod1 , Tal1 , Bhlhe22 , Neurod2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 910
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 827
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Erf , Elk1 , Fli1 , Gm5454 , Etv5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 814
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zfp281 , Zfp148 , Maz , Sp3 , Sp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 768
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sox3 , Sox17 , Sox6 , Sox9 , Sox4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 737
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Rfx2 , Arid2 , Rfx4 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 703
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfia , Nfix , Nfib , Nfic
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 553
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 374
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfeb , Bach2 , Tcfec , Srebf1 , Mitf
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 335
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
9430076C15Rik , Creb3 , Batf3 , Atf7 , Atf2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 283
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 273
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tbpl2 , Sox2 , Pou5f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 232
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Mbtps2 , Yy1 , Wt1 , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 195
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 81
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mef2a , Mef2c , Mef2d , Mef2b , Tead4
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_245-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_245-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_245-naivegw

No motifs with negative importance