54_LNG_A

In [1]:

# Parameters
sample_name = "LNG;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_54-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_54-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 17:49:01,660 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	Lung
Cell Group	Other 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	97256	53090	7.1397	66919568	2747223	0.0411	3894814	0.0582	20739010	0.31
rep2	97256	53090	14.3428	18521142	2846649	0.1538	2837042	0.1533	7068055	0.382

Modelling Metadata

Metric	Value
auPRC	0.6613
Calibrated Recall at 50% FDR	0.163
Number of Positive Examples in Test Data	58105
Number of Negative Examples in Test Data	8012746
Imbalance Ratio in Test Data	0.0072
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

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Myod1		absent
Irf1		absent
Ets1		absent
Foxc1		absent
Nfia		absent
Tcfeb		absent
Rfx1		absent
Fos		absent
Smarcc2		absent
Grhl1		absent
Foxi1		absent
Rfx8		absent
Mbtps2		absent
Creb3		absent
Klf16		absent
Sp3		absent
Cebpb		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Pbx3	absent
Zfp143	absent
Klf2	absent
Elk3	absent
Stat1	absent
Yy1	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_54-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_54-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_54-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_1, # patterns: 27, # seqlets: 19855, Positive for: LNG;A;CL

pattern_0: # seqlets: 3248
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp5 , Sp2 , Klf16 , Klf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 2758
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 2211
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ets1 , Elk1 , Etv6 , Fli1 , Elk3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1504
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxi1 , Pbx3 , Nfya , Ybx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1307
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 972
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Yy1 , Sp3 , Wt1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 921
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfia , Nfib , Nfix , Nfic
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 820
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxc1 , Foxf2 , Foxc2 , Foxb1 , Foxa2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 774
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Cebpb , Cebpa , Cebpd , Cebpg , Cebpe
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 711
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Klf16 , Klf14 , Sp8 , Sp5 , Klf7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 645
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 641
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 638
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Creb3 , 9430076C15Rik , Atf7 , Jdp2 , Atf2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 502
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Smarcc1 , Fosb , Nfe2l2 , Nfe2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 493
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfeb , Bach2 , Tcfec , Mitf , Tcfe3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 343
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf1 , Prdm1 , Stat2 , Irf4 , Bcl11a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 187
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Zfx , E2f1 , Zbtb7a , Sp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 177
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Zfx , Ctcfl , Sp2 , Tcfap2d
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 149
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Wt1 , Zfx , Mbd2 , Tcfap2d
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 135
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Rfx2 , Arid2 , Rfx4 , Rfx3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 130
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Myod1 , Ascl2 , Tcf4 , Tcf12 , Myog
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_21: # seqlets: 112
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx8 , Rfx5 , Rfx3 , Rfx7 , Rfx4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_22: # seqlets: 108
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_23: # seqlets: 109
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Zfx , Zbtb7a , Sp2 , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_24: # seqlets: 92
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , E2f1 , Zbtb7a , Egr4 , Wt1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_25: # seqlets: 84
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Zfx , Wt1 , Zbtb7a , Sp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_26: # seqlets: 84
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Grhl1 , Tcfcp2
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_54-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_54-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_54-naivegw
Displaying motifs which has negative importances for the cell type

metacluster_0, # patterns: 25, # seqlets: 11396, Negative for: LNG;A;CL

pattern_0: # seqlets: 2153
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zbtb7b , Glis1 , Glis2 , Zbtb7a , Gli1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 1339
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zeb1 , Snai2 , Id4 , Mesp2 , Twist1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1261
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1155
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ahctf1 , Arid3b , Onecut1 , Onecut3 , Dbx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1139
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 811
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 791
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 419
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ppara , Rxra , Rarb , Esrra , Esrrg
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 312
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , E2f1 , Tcfap2d , Zbtb7a , Sp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 280
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hoxb1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 271
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxd3 , Onecut2 , Runx2 , Foxm1 , Foxj1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 189
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sfpi1 , Bcl11a , Spib , Spic , Ets1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 177
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 154
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pitx2 , AC189028.1 , Nr5a2 , Pitx3 , Obox5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 132
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfe2l2 , Nfe2 , Fos , Jund , Smarcc1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 118
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2 , Zbtb7a , Nr6a1 , Sp1 , Nr5a1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 129
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 116
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , E2f1 , Zfx , Zbtb7a , Tcfap2d
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 98
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 78
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Esrrg , Nr5a1 , Esrrb , Nr4a1 , Ppara
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 69
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_21: # seqlets: 66
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1 , Zfp143 , Myc
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_22: # seqlets: 53
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , E2f1 , Wt1 , Sp2 , Zfx
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_23: # seqlets: 49
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_24: # seqlets: 37
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a1
Sequence
Contrib Scores
Hyp_Contrib Scores