224_LVR_8wks_D

In [1]:

# Parameters
sample_name = "LVR;8wks;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_224-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_224-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 02:39:13,107 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	Liver(adult-8wks)
Cell Group	Other 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	189092	141583	10.5019	17456519	3823117	0.2192	1593713	0.0914	6980539	0.4002
rep10	189092	141583	9.0657	32667634	6614408	0.2025	3033830	0.0929	12195644	0.3734
rep11	189092	141583	18.336	15179717	5834213	0.3845	2643969	0.1742	6819720	0.4494
rep12	189092	141583	16.7853	22681444	9236183	0.4074	3669106	0.1618	10426106	0.4598
rep13	189092	141583	10.1592	29558474	4476333	0.1515	2304623	0.078	11267615	0.3813
rep14	189092	141583	12.0208	27381052	7358853	0.2689	2687758	0.0982	11334053	0.4141
rep2	189092	141583	7.0062	113906602	34245186	0.3007	10570447	0.0928	47552662	0.4175
rep3	189092	141583	11.7577	19823261	5348148	0.2699	2058410	0.1039	8467563	0.4273
rep4	189092	141583	11.3708	17752601	4238100	0.2389	1874130	0.1056	7408898	0.4176
rep5	189092	141583	15.65	16038825	7047902	0.4396	2508806	0.1565	7917819	0.4939
rep6	189092	141583	13.2908	16127786	6775612	0.4203	2264582	0.1405	7864700	0.4879
rep7	189092	141583	11.1194	17614444	6972538	0.396	2422528	0.1376	8073995	0.4585
rep8	189092	141583	17.6579	19263658	6937639	0.3603	2876396	0.1494	8616200	0.4475
rep9	189092	141583	15.7119	21092484	6312055	0.2994	2745382	0.1302	9126180	0.4329

Modelling Metadata

Metric	Value
auPRC	0.5399
Calibrated Recall at 50% FDR	0.252
Number of Positive Examples in Test Data	179928
Number of Negative Examples in Test Data	7890923
Imbalance Ratio in Test Data	0.0223
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
Hnf4g
Ctcf
Sp3

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Erf		absent
Cebpb		absent
Mbtps2		absent
Foxa2		absent
Bach2		absent
Smarcc2		absent
Onecut3		absent
Bach1		absent
Pbx3		absent
Hsf1		absent
9430076C15Rik		absent
Irf1		absent
Nfia		absent
Foxd3		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Nfic	absent
Foxc1	absent
Tcfeb	absent
Zfp143	absent
Cebpa	absent
Onecut1	absent
Gabpa	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_224-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_224-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_224-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_0, # patterns: 21, # seqlets: 24957, Positive for: LVR;8wks;D;En

pattern_0: # seqlets: 4545
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hnf4g , Nr1h2 , Pparg , Ppard , Nr4a3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 3858
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 3232
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Cebpb , Cebpa , Cebpd , Cebpg , Cebpe
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 2314
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp5 , Sp2 , Klf16 , Klf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1978
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfia , Nfix , Nfib , Nfic
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1172
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 961
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Onecut3 , Onecut1 , Onecut2 , Sox8
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 896
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1 , Dux
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 825
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Erf , Gabpa , Nr2c2 , Ets2 , Etv5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 803
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 720
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Bach2 , Tcfeb , Tcfec , Mitf , Srebf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 639
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
9430076C15Rik , Creb3 , Atf7 , Atf2 , Creb1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 587
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxa2 , Foxf2 , Foxa3 , Foxc2 , Foxc1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 530
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxa2 , Foxa1 , Foxb1 , Foxc1 , Foxf2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 471
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxd3 , Foxa3 , Foxn3 , Foxm1 , Foxp4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 442
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Yy1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 341
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 334
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf1 , Prdm1 , Stat2 , Irf2 , Bcl11a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 158
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Bach1 , Nfe2 , Nfe2l2 , Smarcc1 , Fos
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 101
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 50
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3
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_224-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_224-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_224-naivegw

No motifs with negative importance