66_NRV_Eye-OPTC_A

In [1]:

# Parameters
sample_name = "NRV;Eye-OPTC;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_66-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_66-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 18:26:41,181 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	Eye- Optic nerve
Cell Group	Neural Cells and Tissues
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	70145	43626	5.378	124434468	5745645	0.0462	7041856	0.0566	40602490	0.3263

Modelling Metadata

Metric	Value
auPRC	0.6751
Calibrated Recall at 50% FDR	0.174
Number of Positive Examples in Test Data	52456
Number of Negative Examples in Test Data	8018395
Imbalance Ratio in Test Data	0.0065
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
Sp3

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Mbtps2		absent
Irf1		absent
Bach2		absent
Foxi1		absent
Creb3		absent
Fos		absent
Sox6		absent
Tbpl2		absent
Elk1		absent
Smarcc2		absent
Mef2d		absent
Nfia		absent
Rfx1		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
E4f1	absent
Pbx3	absent
Hes7	absent
Maz	absent
Gabpa	absent
Zfp143	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_66-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_66-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_66-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_0, # patterns: 21, # seqlets: 20824, Positive for: NRV;Eye-OPTC;A;CL

pattern_0: # seqlets: 2726
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 2325
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Zbtb7a , Zfp148 , Sp5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1714
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sox6 , Sox3 , Sox17 , Sox9 , Sox4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1696
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1628
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Klf16 , Sp1 , Klf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1610
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxi1 , Pbx3 , Nfya , Ybx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 1503
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Elk1 , Elk3 , Ets1 , Erf , Elk4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 1495
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Creb3 , Jdp2 , Atf7 , 9430076C15Rik , Batf3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 1356
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfia , Nfix , Nfib , Nfic , Insm1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 1010
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Sp3 , Yy1 , Wt1 , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 853
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Rfx2 , Arid2 , Rfx4 , Rfx3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 695
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Bach2 , Tcfeb , Tcfec , Mitf , Usf2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 637
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Zfp143 , Tbx2 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 400
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf1 , Irf4 , Prdm1 , Stat2 , Irf2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 393
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Smarcc1 , Fosb , Bach1 , Nfe2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 208
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 147
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tbpl2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 129
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mef2d , Mef2b , Mef2c , Mef2a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 114
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , E2f1 , Wt1 , Zbtb7a , Zfx
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 107
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Wt1 , E2f1 , Zbtb7a , Sp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 78
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Zbtb7a , E2f1 , Zfx , Sp2
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_66-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_66-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_66-naivegw

No motifs with negative importance