229_wES_LNG_E14.5_D

In [1]:

# Parameters
sample_name = "wES;LNG;E14.5;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_229-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_229-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 02:54:16,115 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	Mouse lung (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	251504	176183	8.7247	174947722	NA	NA	NA	NA	NA	NA

Modelling Metadata

Metric	Value
auPRC	0.611
Calibrated Recall at 50% FDR	0.231
Number of Positive Examples in Test Data	119397
Number of Negative Examples in Test Data	7951454
Imbalance Ratio in Test Data	0.0148
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
Rest
Pbx3
Nfia
Sp3
Ctcf

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Creb3		absent
Grhl1		absent
Irf1		absent
Hsf1		absent
Erg		absent
Smarcc2		absent
Rfx1		absent
Mef2a		absent
E2f1		absent
Cebpb		absent
Tcf21		absent
Gm5294		absent
Fos		absent
Mbtps2		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Foxd1	absent
Ascl2	absent
Zfp143	absent
Elk1	absent
E4f1	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_229-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_229-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_229-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_1, # patterns: 24, # seqlets: 20893, Positive for: wES;LNG;E14.5;D;En

pattern_0: # seqlets: 3858
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 3833
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Sp5 , Klf16 , Klf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 2386
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Erg , Ets1 , Erf , Etv5 , Gabpa
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1680
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfia , Nfix , Nfib , Nfic , Rfx3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1375
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
E2f1 , Tcfap2c , Tcfap2d
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1169
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gm5294 , Foxp2 , Foxp4 , Foxj2 , Foxj3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 1098
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcf21 , Ascl2 , Atoh8 , Tcfap4 , Figla
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 839
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 823
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 595
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Creb3 , 9430076C15Rik , Batf3 , Jdp2 , Atf7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 588
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 497
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Rfx2 , Arid2 , Rfx4 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 366
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Cebpb , Cebpd , Cebpa , Cebpg , Cebpe
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 366
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Yy1 , Sp3 , Wt1 , Egr4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 330
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 174
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mef2a , Mef2c , Mef2d , Mef2b
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 158
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Nfe2l2 , Nfe2 , Fosb , Smarcc1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 155
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rest
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 152
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 140
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf1 , Stat2 , Irf4 , Prdm1 , Irf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 118
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_21: # seqlets: 101
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_22: # seqlets: 59
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Grhl1 , Tcfcp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_23: # seqlets: 33
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
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_229-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_229-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_229-naivegw
Displaying motifs which has negative importances for the cell type

metacluster_0, # patterns: 16, # seqlets: 9643, Negative for: wES;LNG;E14.5;D;En

pattern_0: # seqlets: 2349
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Snai2 , Zeb1 , Id4 , Mesp2 , Atoh8
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 1323
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zic5 , Glis1 , Zbtb7b , Zic4 , Glis2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1097
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hic1 , Hic2 , Nfic
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1058
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 835
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rarb , Rxra , Ppara , Rara , Nr2f6
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 697
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 676
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 579
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gata4 , Gata2 , Gata1 , Gata6 , Gata3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 464
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 143
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Erg , Ets1 , Fev , ENSMUSG00000044690 , Elf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 137
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxc1 , Foxc2 , Foxb1 , Foxa2 , Foxa1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 76
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxd3 , Foxm1 , Foxj1 , Foxn3 , Foxp4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 73
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2 , Hsf1 , Nr6a1 , Esrrb
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 56
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2 , Esrrb
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 43
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2 , Pitx2 , AC189028.1 , Pitx3 , Esrrb
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 37
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2
Sequence
Contrib Scores
Hyp_Contrib Scores