267_3134_mammaryADNCRCNM_D

In [1]:

# Parameters
sample_name = "3134_mammaryADNCRCNM;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_267-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_267-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 04:47:16,227 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	murine mammary adenocarcinoma cell line(3134 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	136947	87930	39.7157	7022509	3158182	0.4505	2694533	0.3843	2403668	0.3428
rep10	136947	87930	51.924	3344251	1660300	0.4976	1507126	0.4517	1007425	0.3019
rep11	136947	87930	52.7641	1683810	793890	0.4731	732623	0.4366	510951	0.3045
rep12	136947	87930	48.1718	4780497	2252146	0.472	2052191	0.4301	1566738	0.3283
rep13	136947	87930	46.5175	2835281	1247933	0.4413	1141920	0.4038	893689	0.3161
rep14	136947	87930	44.3893	4971237	2291935	0.4619	2076763	0.4185	1655971	0.3337
rep15	136947	87930	35.2295	7797335	3215586	0.413	2644421	0.3397	2792796	0.3587
rep16	136947	87930	46.6652	5100968	2377739	0.467	2157205	0.4237	1679845	0.3299
rep17	136947	87930	24.9076	19159043	6871250	0.3589	5042892	0.2634	7220983	0.3772
rep18	136947	87930	47.8135	2858030	1279884	0.449	1168537	0.41	896454	0.3145
rep19	136947	87930	47.9708	4971910	2347831	0.473	2142269	0.4316	1630381	0.3285
rep2	136947	87930	48.6307	2648207	1172874	0.4441	1086552	0.4114	828750	0.3138
rep20	136947	87930	34.7946	7722377	3084741	0.4001	2523956	0.3274	2777587	0.3602
rep21	136947	87930	45.3599	3001479	1324939	0.4426	1198167	0.4003	953087	0.3184
rep22	136947	87930	31.076	4540686	1316707	0.2907	1223197	0.27	1547199	0.3416
rep23	136947	87930	38.5522	7107385	3220800	0.4539	2730465	0.3848	2473363	0.3485
rep24	136947	87930	42.1188	5839738	2557450	0.4388	2270971	0.3896	1963387	0.3368
rep25	136947	87930	47.5765	2932897	1309790	0.4478	1188598	0.4063	923903	0.3158
rep26	136947	87930	48.4718	5071643	2419180	0.4778	2188589	0.4323	1664241	0.3287
rep27	136947	87930	37.4407	7228337	2793365	0.3871	2390140	0.3312	2520360	0.3492
rep28	136947	87930	13.5389	7941050	890403	0.1123	742979	0.0937	2469225	0.3113
rep29	136947	87930	20.7642	1178337	142885	0.1217	157894	0.1345	368151	0.3136
rep3	136947	87930	45.1851	4855881	2292723	0.473	2084615	0.43	1608971	0.3319
rep4	136947	87930	35.8257	7443213	2948031	0.3967	2439702	0.3283	2683273	0.3611
rep5	136947	87930	34.7476	7583068	2983657	0.3941	2450589	0.3237	2735388	0.3613
rep6	136947	87930	46.623	2927897	1303710	0.4465	1183546	0.4053	925520	0.3169
rep7	136947	87930	30.5213	4506228	1273126	0.2832	1167704	0.2598	1536587	0.3418
rep8	136947	87930	39.9602	6496648	2806424	0.4328	2443816	0.3768	2215799	0.3417
rep9	136947	87930	39.9044	6923108	3060999	0.4429	2647650	0.3831	2354191	0.3406

Modelling Metadata

Metric	Value
auPRC	0.5918
Calibrated Recall at 50% FDR	0.226
Number of Positive Examples in Test Data	112426
Number of Negative Examples in Test Data	7958425
Imbalance Ratio in Test Data	0.0139
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
Fos
Runx2
Ctcf
Creb3
Pbx3
Mbtps2
Nfia

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Ebf1		absent
Cebpb		absent
Mef2d		absent
Bach2		absent
Sp3		absent
Srf		absent
Erf		absent
Hsf1		absent
Rela		absent
Creb1		absent
Irf1		absent
Ctcfl		absent
Smarcc2		absent
Rfx2		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Gabpa	absent
Sp5	absent
Zfp143	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_267-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_267-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_267-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_0, # patterns: 28, # seqlets: 17937, Positive for: 3134_mammaryADNCRCNM;D;En

pattern_0: # seqlets: 2520
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 2473
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Klf16 , Sp5 , Klf5 , Sp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 2162
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Smarcc1 , Jund , Fosb , Nfe2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1714
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfia , Nfib , Nfix , Nfic
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1499
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Erf , Erg , Ets1 , Etv5 , Gabpa
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 984
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 963
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1 , Dux
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 765
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Runx2 , Runx1 , Runx3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 561
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , E2f1 , Sp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 476
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Creb1 , Jdp2 , 9430076C15Rik , Atf2 , Atf7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 468
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Creb3 , Batf3 , 9430076C15Rik , Atf7 , Atf2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 413
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Sp3 , Yy1 , Wt1 , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 391
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Cebpb , Cebpd , Cebpa , Cebpg , Cebpe
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 365
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf1 , Prdm1 , Stat2 , Irf2 , Irf4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 324
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Zfp143 , Tbx2 , Six5 , Zfp523
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 261
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcfl , Tcfap2d , Sp3 , Egr4 , Tcfap2c
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 254
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 238
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Bach2 , Tcfeb , Tcfec , Mitf , Tcfe3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 156
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ebf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 150
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 141
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_21: # seqlets: 151
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mef2d , Mef2a , Mef2c , Mef2b
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_22: # seqlets: 111
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx2 , Rfx1 , Arid2 , Rfx4 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_23: # seqlets: 99
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Zfx , Wt1 , Sp2 , Klf15
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_24: # seqlets: 89
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rela , Relb , Nfkb1 , Rel , Hivep1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_25: # seqlets: 89
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , E2f1 , Tcfap2d , Zfx , Sp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_26: # seqlets: 83
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , E2f1 , Ctcfl , Tcfap2d , Zfx
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_27: # seqlets: 37
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Srf , Neurod1
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_267-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_267-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_267-naivegw

No motifs with negative importance