70_BRN_MDL_OBLNGT_A

In [1]:

# Parameters
sample_name = "BRN;MDL_OBLNGT;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_70-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_70-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 18:39:28,217 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	Brain- Medulla Oblongata
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	87447	47590	9.4114	11977761	355140	0.0297	876467	0.0733	3913495	0.3273
rep2	87447	47590	11.4626	41196844	3759560	0.0913	3908200	0.0949	14884486	0.3615

Modelling Metadata

Metric	Value
auPRC	0.671
Calibrated Recall at 50% FDR	0.182
Number of Positive Examples in Test Data	56390
Number of Negative Examples in Test Data	8014461
Imbalance Ratio in Test Data	0.007
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
Pbx3
Ctcf
Sp3

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Rfx8		absent
Tbpl2		absent
Nfia		absent
Fos		absent
Smarcc2		absent
Sox9		absent
Ets1		absent
Irf1		absent
Creb3		absent
Mef2b		absent
Tef		absent
Mbtps2		absent
Tcfec		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Zfp143	absent
Gabpa	absent
Maz	absent
Mbd1	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_70-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_70-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_70-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_1, # patterns: 24, # seqlets: 21642, Positive for: BRN;MDL_OBLNGT;A;CL

pattern_0: # seqlets: 4772
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 2188
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Sp5 , Klf16 , Klf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1763
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1630
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1578
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sox9 , Sox6 , Sox17 , Sox3 , Sox4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1354
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Zfp148 , Zfp281 , Zbtb7a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 1352
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfia , Nfix , Nfib , Rfx3 , Nfic
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 1207
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ets1 , Gabpa , Elk3 , Erf , Etv4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 938
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Creb3 , 9430076C15Rik , Atf7 , Jdp2 , Batf3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 793
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Yy1 , Sp3 , Wt1 , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 684
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Rfx2 , Arid2 , Rfx4 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 656
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 602
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfec , Tcfeb , Bach2 , Mitf , Tcfe3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 470
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Smarcc1 , Fosb , Nfe2 , Jund
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 395
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tbpl2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 286
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Ctcfl , Wt1 , Zfx , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 259
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx8 , Rfx3 , Rfx5 , Rfx7 , Rfx4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 189
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , E2f1 , Tcfap2d , Zfx , Wt1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 113
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf1 , Prdm1 , Stat2 , Irf2 , Irf4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 102
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mef2b , Mef2d , Mef2c , Mef2a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 97
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Ctcfl , Wt1 , E2f1 , Zbtb7a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_21: # seqlets: 94
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tef , Dbp , Nfil3 , Hlf
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_22: # seqlets: 78
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Wt1 , Zfx , Egr4 , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_23: # seqlets: 42
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Wt1 , Zfx , Klf15 , Ctcfl
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_70-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_70-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_70-naivegw
Displaying motifs which has negative importances for the cell type

metacluster_0, # patterns: 18, # seqlets: 8596, Negative for: BRN;MDL_OBLNGT;A;CL

pattern_0: # seqlets: 1635
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zeb1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 1456
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Arid3b , Onecut1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1194
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Glis2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 967
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr1i3 , Nr1h2 , Ppara , Hnf4g , Rxra
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 877
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Myc , Twist2 , Bhlha15 , Neurog3 , Olig1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 709
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2 , Nr6a1 , Esrrb , Nr5a1 , Hsf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 369
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 341
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Wt1 , Zfx , Zbtb7a , Zfp148
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 195
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Zfx , Zbtb7a , Wt1 , Egr4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 163
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 133
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hoxc9 , Hoxa9 , Cdx4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 117
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 94
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Wt1 , Sp3 , Klf15 , Maz , Egr2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 79
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pitx2 , AC189028.1 , Pitx3 , Obox5 , Otx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 90
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 70
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2 , Pitx2 , AC189028.1 , Pitx3 , Obox5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 51
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Maz , Zfp281
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 56
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores