244_Muller_P12_D

In [1]:

# Parameters
sample_name = "Muller;P12;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_244-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_244-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 03:34:41,198 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	Muller cell(P12)
Cell Group	Neural Cells and 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	277130	206968	9.2293	157227576	NA	NA	NA	NA	NA	NA
rep2	277130	206968	12.0745	109702032	31529181	0.2875	10237389	0.0933	50715528	0.4624
rep3	277130	206968	8.4813	172661149	NA	NA	NA	NA	NA	NA

Modelling Metadata

Metric	Value
auPRC	0.6502
Calibrated Recall at 50% FDR	0.214
Number of Positive Examples in Test Data	252010
Number of Negative Examples in Test Data	7818841
Imbalance Ratio in Test Data	0.0312
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
Nfic
Rest
Ctcf
Fos
Smarcc2

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Mef2d		absent
Nfia		absent
Cebpb		absent
Irf1		absent
Ets1		absent
Lhx2		absent
Sp3		absent
Runx1		absent
Mbtps2		absent
Pbx3		absent
Sox17		absent
Srf		absent
Hsf1		absent
Rora		absent
Tcfec		absent
Rfx1		absent
Batf3		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Sp2	absent
Nfya	absent
9430076C15Rik	absent
Esx1	absent
Runx2	absent
Cebpd	absent
Tcfeb	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_244-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_244-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_244-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_1, # patterns: 26, # seqlets: 21029, Positive for: Muller;P12;D;En

pattern_0: # seqlets: 2978
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Jund , Fosb , Smarcc1 , Nfe2l2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 2865
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 2197
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1751
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Sp5 , Klf16 , Klf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1278
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfic
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1265
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Lhx2 , Lhx9 , Emx2 , Rax , Arx
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 1215
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfia , Nfix , Nfib , Nfic
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 1129
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sox17 , Sox3 , Sox6 , Sox9 , Sox4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 904
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Cebpb , Cebpa , Cebpd , Cebpg , Dbp
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 829
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ets1 , Etv6 , Erf , Elk1 , Fli1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 807
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Runx1 , Runx2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 713
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Batf3 , 9430076C15Rik , Creb3 , Atf7 , Atf2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 571
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 536
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rora , 9430076C15Rik , Rorc , Creb1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 495
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Arid2 , Rfx2 , Rfx4 , Rfx5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 469
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 222
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf1 , Prdm1 , Stat2 , Irf2 , Bcl11a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 199
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfec , Tcfeb , Bach2 , Mitf , Tcfe3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 128
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mef2d , Mef2b , Mef2c , Mef2a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 120
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 110
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Yy1 , Sp3 , Wt1 , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_21: # seqlets: 70
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rest
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_22: # seqlets: 50
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_23: # seqlets: 48
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mef2d , Mef2a , Mef2c , Mef2b
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_24: # seqlets: 38
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Srf
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_25: # seqlets: 42
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
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_244-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_244-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_244-naivegw
Displaying motifs which has negative importances for the cell type

metacluster_0, # patterns: 27, # seqlets: 10955, Negative for: Muller;P12;D;En

pattern_0: # seqlets: 1816
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 1396
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zbtb7b , Glis2 , Zbtb7a , Glis1 , Zic5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1390
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zfp637
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1223
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zfp238 , Tcf4 , Twist2 , Bhlha15 , Tcf21
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1055
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 922
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Onecut1 , Onecut2 , Onecut3 , Cux2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 570
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sox6 , Sox17 , Sox9
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 428
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfe2l2 , Nfe2 , Jund , Batf , Fos
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 302
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 283
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gata2 , Gata4 , Gata1 , Gata6 , Mecom
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 239
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Runx1 , Runx2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 154
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ppara , Esrrg , Nr4a2 , Rxra , Nr1h2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 131
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxd3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 116
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 100
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pitx2 , AC189028.1 , Pitx3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 96
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Dux , Foxi1 , Duxbl , Cphx , Lhx6
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 79
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Onecut3 , Onecut1 , Onecut2 , Sox7 , Sox18
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 94
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1 , Zfp143
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 80
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2 , Esrrb , Nr6a1 , Nr5a1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 70
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 66
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_21: # seqlets: 64
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Alx3 , Dbx1 , Esx1 , Prop1 , Lhx3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_22: # seqlets: 63
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxd3 , Onecut2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_23: # seqlets: 61
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Cebpb , Cebpa , Cebpg , Cebpd , Dbp
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_24: # seqlets: 57
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2 , Pitx2 , AC189028.1 , Pitx3 , Obox5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_25: # seqlets: 59
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nr5a2 , Nr6a1 , Esrrb , Nr5a1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_26: # seqlets: 41
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Cebpb , Cebpg , Cebpa , Cebpd
Sequence
Contrib Scores
Hyp_Contrib Scores