269_A20_B-lymphoma_D

In [1]:

# Parameters
sample_name = "A20;B-lymphoma;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_269-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_269-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 04:54:26,366 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	Murine B-lymphoma cell line(A20 cell line)
Cell Group	Cancer or Immortalized cells
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	177830	149198	18.0012	10987474	2513748	0.2292	2308867	0.2105	4000423	0.3647
rep10	177830	149198	18.2361	10932212	2524431	0.2313	2309069	0.2116	3980864	0.3647
rep11	177830	149198	18.1804	10974464	2506120	0.2287	2309398	0.2108	3992387	0.3644
rep12	177830	149198	17.831	10898142	2458558	0.226	2265225	0.2082	3971124	0.365
rep13	177830	149198	17.6211	10922703	2451217	0.2248	2270340	0.2082	3977698	0.3648
rep14	177830	149198	18.1906	10808248	2694547	0.2497	2289835	0.2122	3938728	0.365
rep15	177830	149198	15.5067	3300423	510167	0.1549	589932	0.1792	1194854	0.3629
rep16	177830	149198	8.1824	26514251	4658672	0.1758	3162251	0.1193	9497873	0.3584
rep2	177830	149198	17.9871	10987502	2464561	0.2247	2293891	0.2091	4002795	0.3649
rep3	177830	149198	17.8915	10943898	2508845	0.2296	2285917	0.2092	3986710	0.3649
rep4	177830	149198	16.0158	4891333	853020	0.175	933905	0.1916	1795142	0.3682
rep5	177830	149198	18.4378	10475072	2621498	0.2507	2242126	0.2144	3837453	0.367
rep6	177830	149198	18.3476	10402272	2607499	0.2511	2241019	0.2158	3816572	0.3675
rep7	177830	149198	18.9656	9574445	2721278	0.2846	2138643	0.2237	3543635	0.3707
rep8	177830	149198	12.0798	20809534	4378547	0.2106	3316071	0.1595	7664471	0.3687
rep9	177830	149198	20.9909	4469992	949107	0.2131	1013266	0.2275	1612032	0.3619

Modelling Metadata

Metric	Value
auPRC	0.5745
Calibrated Recall at 50% FDR	0.2
Number of Positive Examples in Test Data	163470
Number of Negative Examples in Test Data	7907381
Imbalance Ratio in Test Data	0.0203
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
Sfpi1

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Rest		absent
Smarcc2		absent
Gabpa		absent
Tbpl2		absent
Zfx		absent
Sp3		absent
Bcl11a		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Mbtps2	absent
Pbx3	absent
Srebf2	absent
Foxd3	absent
Bhlhe40	absent
Zfp143	absent
Klf2	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_269-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_269-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_269-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_1, # patterns: 13, # seqlets: 33246, Positive for: A20;B-lymphoma;D;En

pattern_0: # seqlets: 21092
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 4682
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Bcl11a , Irf1 , Sfpi1 , Prdm1 , Zscan10
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 2803
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sfpi1 , Bcl11a , Spib , Ets1 , Erg
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 2706
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Thrb
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 743
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 371
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gabpa , Sp3 , Erf , Elk3 , Etv4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 223
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Zbtb7a , Wt1 , E2f1 , Sp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 168
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rest
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 157
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Wt1 , E2f1 , Zfx , Zbtb7a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 117
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 79
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tbpl2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 69
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , E2f1 , Wt1 , Tcfap2d , Zbtb7a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 36
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zfx , Sp3 , Sp2 , Maz , Wt1
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_269-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_269-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_269-naivegw
Displaying motifs which has negative importances for the cell type

metacluster_0, # patterns: 14, # seqlets: 6453, Negative for: A20;B-lymphoma;D;En

pattern_0: # seqlets: 1305
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Glis2 , Zbtb7b , Glis1 , Zbtb7a , Zic5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 1234
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rreb1 , Maz , Sp3 , Zfp281 , Zfp148
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 997
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ferd3l , Tcf3 , Ascl2 , Tcf4 , Myod1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 700
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Dbx1 , Tlx2 , Arid3b , Esx1 , Pou1f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 408
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 287
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pitx2 , AC189028.1 , Pitx3 , Obox5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 284
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Bcl6
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 267
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 261
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 226
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc1 , Fos , Fosb , Nfe2l2 , Nfe2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 150
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tbpl2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 138
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 113
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxd3 , Foxj1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 83
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mef2a , Mef2c , Mef2b , Mef2d
Sequence
Contrib Scores
Hyp_Contrib Scores