19_BSPHL_A

In [1]:

# Parameters
sample_name = "BSPHL;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_19-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_19-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 16:04:28,929 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	basophils
Cell Group	Other Immune Cells
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	174457	144811	26.825	12962452	7488055	0.5785	4642303	0.3586	5768483	0.4456
rep2	174457	144811	28.2415	10487771	6040733	0.5769	3826702	0.3655	4635920	0.4428
rep3	174457	144811	16.6966	33036477	16660505	0.5046	7634688	0.2312	14951421	0.4528
rep4	174457	144811	23.1443	17160668	9900039	0.5775	5843636	0.3409	7655375	0.4466

Modelling Metadata

Metric	Value
auPRC	0.6121
Calibrated Recall at 50% FDR	0.212
Number of Positive Examples in Test Data	169357
Number of Negative Examples in Test Data	7901494
Imbalance Ratio in Test Data	0.021
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

Common Motifs

Motif Name	Modisco	Homer
Pbx3
Mbtps2
Ctcf

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Gata1		absent
Wt1		absent
Sp3		absent
Nfix		absent
Runx1		absent
Rfx1		absent
Tcfeb		absent
Ctcfl		absent
Stat5a		absent
Klf16		absent
Smarcc2		absent
Erg		absent
9430076C15Rik		absent
Nfe2		absent
Irf1		absent
Sfpi1		absent
Cebpb		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Cebpg	absent
Elk1	absent
Atf6	absent
Gata4	absent
Sp2	absent
Fos	absent
Zfp143	absent
Hes7	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_19-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_19-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_19-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_1, # patterns: 23, # seqlets: 25388, Positive for: BSPHL;A;CL

pattern_0: # seqlets: 5561
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sfpi1 , Ets1 , Erg , Bcl11a , Etv6
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 4727
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 2665
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfe2 , Smarcc1 , Nfe2l2 , Fos , Bach1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 2283
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Cebpb , Cebpa , Cebpd , Cebpg , Cebpe
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1898
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp5 , Sp2 , Klf16 , Klf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1115
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 1050
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Runx1 , Runx2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 869
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
9430076C15Rik , Creb3 , Atf7 , Atf2 , Jdp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 856
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gata1 , Gata4 , Gata2 , Mecom , Gata6
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 697
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf1 , Stat2 , Prdm1 , Irf2 , Irf4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 680
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 589
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Klf16 , Klf14 , Sp8 , Sp5 , Klf7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 560
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Yy1 , Sp3 , Wt1 , Zbtb7a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 397
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Zfp143 , Tbx2 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 370
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Erg , Ets1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 331
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfeb , Bach2 , Tcfec , Mitf , Tcfe3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 206
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Wt1 , Sp3 , Zfx , Ctcfl , Sp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 183
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Rfx2 , Arid2 , Rfx4 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 106
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Zfx , Tcfap2d , Ctcfl , Mbd2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 79
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Stat5a , Stat4 , Stat5b , Stat1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 69
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcfl , Sp3 , Zbtb7a , Sp2 , Zfx
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_21: # seqlets: 60
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcfl , Sp3 , E2f1 , Wt1 , Zfx
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_22: # seqlets: 37
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfix , Nfia , Nfib , Klf16 , Nfic
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_19-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_19-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_19-naivegw
Displaying motifs which has negative importances for the cell type

metacluster_0, # patterns: 21, # seqlets: 10706, Negative for: BSPHL;A;CL

pattern_0: # seqlets: 2168
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tbp , Hmg20b , Arid3b , Onecut1 , Pit1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 1990
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zbtb7b , Glis2 , Glis1 , Zbtb7a , Gli1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1431
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gata2 , Gata4 , Gata1 , Gata6 , Gata3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1379
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zeb1 , Snai2 , Id4 , Mesp2 , Scrt1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 786
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Dbx1 , Tlx2 , Lhx1 , Arid3b , Lhx5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 621
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 543
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfe2l2 , Nfe2 , Jund , Batf , Fos
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 482
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Erg , Ets1 , ENSMUSG00000044690 , Elf5 , Fev
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 280
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Arid2 , Rfx2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 193
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Jdp2 , Atf7 , Atf2 , Crem , Creb1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 146
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Atf7 , Batf3 , Jdp2 , Atf2 , Creb3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 111
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2 , Pitx2 , Pitx3 , AC189028.1 , Obox5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 95
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 87
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 76
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 72
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Batf3 , Creb3 , 9430076C15Rik , Atf7 , Atf2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 64
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Bcl6
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 59
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pitx2 , AC189028.1 , Pitx3 , Obox5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 50
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 43
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 30
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores