0_MPP_A_CL_20k

In [1]:

# Parameters
hyperparameter_group = "_20k_832"
sample_name = "MPP_A_CL"

In [2]:

try:
    reload  # Python 2.7
except NameError:
    try:
        from importlib import reload  # Python 3.4+
    except ImportError:
        from imp import reload  # Python 3.0 - 3.3

In [3]:

modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/modisco2019"
mitra_subdir = "report/test"
task_idx = 0
sample_name = "MPP;A;CL"
task_dir = "task_{0}-naivegw{1}".format(task_idx, hyperparameter_group)

In [4]:

from matlas.modisco_report import report_pipeline
#modisco_report.run_pipeline(sample_name, prepare=False, render=False)

Using TensorFlow backend.
2019-02-26 19:32:04,767 [WARNING] git-lfs not installed

In [5]:

report_pipeline(sample_name, modisco_root, mitra_subdir, task_dir, importance=True)

rsync -t -av /srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/modisco2019/task_0-naivegw_20k_832/tomtomout /srv/www/kundaje/msharmin/report/test/task_0-naivegw_20k_832/
chmod -R +755 /srv/www/kundaje/msharmin/report/test/task_0-naivegw_20k_832

TF-MoDISco is using the TensorFlow backend.

Displaying motifs which has positive importances for the cell type

metacluster_1, # patterns: 22, # seqlets: 11947, Positive for: MPP;A;CL

pattern_0: # seqlets: 3647
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sfpi1 , Spib , Ets1 , Spic , Etv6 , Bcl11a , Etv3 , Fli1 , Gm4881 , Elk1 , Elf4 , Elf2 , Erg , Elk4 , Elk3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 3092
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1092
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp2 , Sp3 , Zbtb7a , Klf5 , Klf16 , Sp5 , Sp1 , Klf14 , Sp8 , Wt1 , Zfp148 , Klf7 , Zfp281 , Klf2 , Egr4 , Sp4 , Klf4 , Klf8 , Klf6 , Klf12 , E2f1 , Tcfap2c , Zfx , Maz , Klf15
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 637
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 492
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Runx2 , Runx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 442
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 302
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfe2l2 , Nfe2 , Bach1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 297
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Creb3 , Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 272
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 252
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf1 , Prdm1 , Stat2 , Irf2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 245
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Bach2 , Tcfeb , Tcfec , Sp3 , Mitf , Tcfe3 , E2f1 , Zfx , Arntl , Mlx , Zbtb7a , Srebf2 , Atf6
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 175
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf1 , Bcl11a , Prdm1 , Sfpi1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 160
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 160
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx2 , Arid2 , Rfx1 , Rfx4 , Rfx7 , Rfx3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 131
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Yy1 , Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 122
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Jdp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 109
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfia , Nfix , Nfib , Nfic
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 107
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Cebpd , Cebpb , Cebpa , Cebpg , Cebpe
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 80
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx8 , Rfx3 , Rfx5 , Rfx4 , Rfx1 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 68
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 33
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_21: # seqlets: 32
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mef2b , Mef2d , Mef2a , Mef2c
Sequence
Contrib Scores
Hyp_Contrib Scores

In [6]:

report_pipeline(sample_name, modisco_root, mitra_subdir, task_dir, importance=False)

rsync -t -av /srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/modisco2019/task_0-naivegw_20k_832/tomtomout /srv/www/kundaje/msharmin/report/test/task_0-naivegw_20k_832/
chmod -R +755 /srv/www/kundaje/msharmin/report/test/task_0-naivegw_20k_832
Displaying motifs which has negative importances for the cell type

metacluster_0, # patterns: 13, # seqlets: 3279, Negative for: MPP;A;CL

pattern_0: # seqlets: 846
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 657
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zeb1 , Snai2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 558
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zbtb7b , Zic5 , Glis1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 331
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 314
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Erg , Ets1 , Etv6 , Sfpi1 , Etv5 , Fli1 , ENSMUSG00000044690 , Etv1 , Etv3 , Elk3 , Etv4 , Bcl11a , Gm5454 , Gm4881 , Elk1 , Elk4 , Erf , Fev , Elf4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 135
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Twist2 , Bhlha15 , Bhlhe22 , Bhlhe23 , Neurog2 , Neurog3 , Olig1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 112
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 80
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 66
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 64
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 42
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Klf2 , Klf1 , Klf4 , Klf8 , Klf12 , Sp5 , Klf14 , Klf5 , Klf7 , Klf16 , Sp8 , Runx2 , Sp1 , Sp2 , Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 34
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 40
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxd3 , Foxj1 , Foxn3
Sequence
Contrib Scores
Hyp_Contrib Scores