# Parameters
data_name = "apTreg;D;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
tomtom_report_root = "http://mitra.stanford.edu/kundaje/msharmin/report/tomtom_outs/cells"
task_dir = "task_209-naivegw"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_209-naivegw/NaiveauPRC.txt"
homer_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_scans"
reportfile = "/mnt/lab_data/kundaje/msharmin/annotations/filtering samples_MS2.xlsx"
sheetname = "filter23"

from matlas.reports import display_metadata

load data from labcluster

Using TensorFlow backend.
2019-08-30 19:28:16,107 [WARNING] git-lfs not installed

display_metadata(data_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	Activated primary T regulatory cells, isolated ex vivo
Cell Group	T cells
Experiment Name	DHS
Experiment Group	GEO

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	138182	116215	5.9779	143353004	33180925	0.2315	18530561	0.1293	53162003	0.3709

Modelling Metadata

Metric	Value
auPRC	0.6033
Calibrated Recall at 50% FDR	0.212
Number of Positive Examples in Test Data	103253
Number of Negative Examples in Test Data	7967598
Imbalance Ratio in Test Data	0.0128
Test Chromosomes	chr2, chr3, chr19

from matlas.reports import display_paiwise_pattern_comparison
from matlas.reports import display_denovo_patterns

display_denovo_patterns(data_name, modisco_root=modisco_root)

TF-MoDISco is using the TensorFlow backend.

The following two links show list of Denovo Patterns and corresponding Motifs discovered by TF-MoDISco

Click here for Denovo Patterns by TF-MoDISco: #8

Pattern Name	TF Name(s)	Modisco
metacluster_1/pattern_0 # seqlets: 14017 SequenceContrib ScoresHyp_Contrib Scores	Ctcf, Ctcfl
metacluster_1/pattern_1 # seqlets: 1129 SequenceContrib ScoresHyp_Contrib Scores
metacluster_1/pattern_2 # seqlets: 1046 SequenceContrib ScoresHyp_Contrib Scores	Etv2, Ets1, Spi1, Erg, Elk1, Spib, Ehf, Elf3, Etv4, Elf1, Gabpa, Elk4, Etv6, Fli1, Etv3, Elk3, Irf4, XP_911724.4, Irf8, Etv1, Etv5, Elf4, Elf2, Spic, Elf5, Fev, Prdm1, Irf3, Spdef
metacluster_1/pattern_3 # seqlets: 732 SequenceContrib ScoresHyp_Contrib Scores	Irf1, Irf2, Stat1, Irf7, Stat2, Irf9, Batf3
metacluster_1/pattern_4 # seqlets: 102 SequenceContrib ScoresHyp_Contrib Scores	Jdp2, Batf, Fosl2, Fosb, Junb, Jun, Jund, Fos, Atf3, Fosl1, Nfe2l2, Bach2, Nfatc1
metacluster_1/pattern_5 # seqlets: 53 SequenceContrib ScoresHyp_Contrib Scores	Zfp143, Tbx2, Thap11, Stat3
metacluster_1/pattern_6 # seqlets: 46 SequenceContrib ScoresHyp_Contrib Scores	T, Rorc
metacluster_1/pattern_7 # seqlets: 41 SequenceContrib ScoresHyp_Contrib Scores	Rest

Click here for Motifs by TF-MoDISco: #58

TF Name	Pattern(s)
Ctcf	Pattern Name Modisco Significance metacluster_1/pattern_0 2.09254e-14 metacluster_1/pattern_1 0.00293923
Ctcfl	Pattern Name Modisco Significance metacluster_1/pattern_0 4.974060000000001e-07 metacluster_1/pattern_1 0.057135000000000005
Etv2	Pattern Name Modisco Significance metacluster_1/pattern_2 7.060310000000001e-05 metacluster_1/pattern_6 0.018559299999999997
Ets1	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00257166 metacluster_1/pattern_6 0.0456245
Spi1	Pattern Name Modisco Significance metacluster_1/pattern_2 0.0370544 metacluster_1/pattern_6 0.0381566
Erg	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00257166 metacluster_1/pattern_6 0.036686699999999996
Elk1	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00257166 metacluster_1/pattern_6 0.0583058
Spib	Pattern Name Modisco Significance metacluster_1/pattern_2 0.000644258 metacluster_1/pattern_3 0.00236355
Ehf	Pattern Name Modisco Significance metacluster_1/pattern_2 0.0303231 metacluster_1/pattern_6 0.050570699999999996
Elf3	Pattern Name Modisco Significance metacluster_1/pattern_2 0.022549200000000002
Etv4	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00463278 metacluster_1/pattern_6 0.021790900000000002
Elf1	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00106377
Gabpa	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00513367 metacluster_1/pattern_6 0.0407209
Elk4	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00355199 metacluster_1/pattern_6 0.0583058
Etv6	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00355199 metacluster_1/pattern_6 0.0120573
Fli1	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00355199 metacluster_1/pattern_6 0.0381566
Etv3	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00355199
Elk3	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00397752 metacluster_1/pattern_6 0.0248876
Irf4	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00355199 metacluster_1/pattern_3 0.0199363
XP_911724.4	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00355199
Irf8	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00355199 metacluster_1/pattern_3 4.3180200000000004e-05
Etv1	Pattern Name Modisco Significance metacluster_1/pattern_2 0.0048786 metacluster_1/pattern_6 0.0248876
Etv5	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00483995 metacluster_1/pattern_6 0.018559299999999997
Elf4	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00566999
Elf2	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00986639 metacluster_1/pattern_6 0.018559299999999997
Spic	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00790418
Elf5	Pattern Name Modisco Significance metacluster_1/pattern_2 0.043557099999999994
Fev	Pattern Name Modisco Significance metacluster_1/pattern_2 0.0140345 metacluster_1/pattern_6 0.0407209
Prdm1	Pattern Name Modisco Significance metacluster_1/pattern_2 0.0145505 metacluster_1/pattern_3 0.000446728
Irf3	Pattern Name Modisco Significance metacluster_1/pattern_2 0.029454400000000006 metacluster_1/pattern_3 0.00223351
Spdef	Pattern Name Modisco Significance metacluster_1/pattern_2 0.043557099999999994
Irf1	Pattern Name Modisco Significance metacluster_1/pattern_3 5.9939e-09
Irf2	Pattern Name Modisco Significance metacluster_1/pattern_3 0.007568000000000001
Stat1	Pattern Name Modisco Significance metacluster_1/pattern_3 2.8692e-06
Irf7	Pattern Name Modisco Significance metacluster_1/pattern_3 4.3180200000000004e-05
Stat2	Pattern Name Modisco Significance metacluster_1/pattern_3 6.40394e-05
Irf9	Pattern Name Modisco Significance metacluster_1/pattern_3 0.00223351
Batf3	Pattern Name Modisco Significance metacluster_1/pattern_3 0.0360824 metacluster_1/pattern_4 0.00189355
Jdp2	Pattern Name Modisco Significance metacluster_1/pattern_4 4.6230599999999996e-06 metacluster_1/pattern_6 0.018559299999999997
Batf	Pattern Name Modisco Significance metacluster_1/pattern_4 0.00017937099999999997 metacluster_1/pattern_6 0.0178092
Fosl2	Pattern Name Modisco Significance metacluster_1/pattern_4 0.00626675 metacluster_1/pattern_6 0.018559299999999997
Fosb	Pattern Name Modisco Significance metacluster_1/pattern_4 0.00155978 metacluster_1/pattern_6 0.018559299999999997
Junb	Pattern Name Modisco Significance metacluster_1/pattern_4 0.017496400000000002 metacluster_1/pattern_6 0.030546499999999997
Jun	Pattern Name Modisco Significance metacluster_1/pattern_4 0.058202 metacluster_1/pattern_6 0.0178092
Jund	Pattern Name Modisco Significance metacluster_1/pattern_4 0.00394352 metacluster_1/pattern_6 0.0248876
Fos	Pattern Name Modisco Significance metacluster_1/pattern_4 0.00209698 metacluster_1/pattern_6 0.0381566
Atf3	Pattern Name Modisco Significance metacluster_1/pattern_4 0.00218776 metacluster_1/pattern_6 0.0220298
Fosl1	Pattern Name Modisco Significance metacluster_1/pattern_4 0.00344027 metacluster_1/pattern_6 0.0381566
Nfe2l2	Pattern Name Modisco Significance metacluster_1/pattern_4 0.00686171
Bach2	Pattern Name Modisco Significance metacluster_1/pattern_4 0.020729499999999998
Nfatc1	Pattern Name Modisco Significance metacluster_1/pattern_4 0.051769
Zfp143	Pattern Name Modisco Significance metacluster_1/pattern_5 7.50483e-09
Tbx2	Pattern Name Modisco Significance metacluster_1/pattern_5 7.50483e-09
Thap11	Pattern Name Modisco Significance metacluster_1/pattern_5 3.10351e-08
Stat3	Pattern Name Modisco Significance metacluster_1/pattern_5 0.028527499999999997
T	Pattern Name Modisco Significance metacluster_1/pattern_6 0.018559299999999997
Rorc	Pattern Name Modisco Significance metacluster_1/pattern_6 0.0248876
Rest	Pattern Name Modisco Significance metacluster_1/pattern_7 1.51099e-14

display_paiwise_pattern_comparison(data_name, modisco_root, homer_root)

Number of CISBP TFs obtained by TF-MoDISco and Homer

Shared TFs between TF-MoDISco and Homer: #33

TF Name	Modisco	Homer
Etv1	Pattern Name Modisco Significance metacluster_1/pattern_2 0.0048786 metacluster_1/pattern_6 0.0248876	Pattern Name Homer Significance motif2.motif 0.0008750380000000001
Erg	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00257166 metacluster_1/pattern_6 0.036686699999999996	Pattern Name Homer Significance motif2.motif 0.0007655639999999999
Fev	Pattern Name Modisco Significance metacluster_1/pattern_2 0.0140345 metacluster_1/pattern_6 0.0407209	Pattern Name Homer Significance motif2.motif 0.000167669
Irf3	Pattern Name Modisco Significance metacluster_1/pattern_2 0.029454400000000006 metacluster_1/pattern_3 0.00223351	Pattern Name Homer Significance motif6.motif 0.0109244
Etv4	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00463278 metacluster_1/pattern_6 0.021790900000000002	Pattern Name Homer Significance motif2.motif 0.00339492
Thap11	Pattern Name Modisco Significance metacluster_1/pattern_5 3.10351e-08	Pattern Name Homer Significance motif7.motif 1.0417700000000001e-06
Irf4	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00355199 metacluster_1/pattern_3 0.0199363	Pattern Name Homer Significance motif6.motif 0.0243433
Elk1	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00257166 metacluster_1/pattern_6 0.0583058	Pattern Name Homer Significance motif2.motif 0.000774308
Elf5	Pattern Name Modisco Significance metacluster_1/pattern_2 0.043557099999999994	Pattern Name Homer Significance motif2.motif 0.023465200000000002
Fli1	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00355199 metacluster_1/pattern_6 0.0381566	Pattern Name Homer Significance motif2.motif 0.0007655639999999999
Etv3	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00355199	Pattern Name Homer Significance motif2.motif 0.0008750380000000001
Irf2	Pattern Name Modisco Significance metacluster_1/pattern_3 0.007568000000000001	Pattern Name Homer Significance motif6.motif 0.039390100000000004
Etv6	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00355199 metacluster_1/pattern_6 0.0120573	Pattern Name Homer Significance motif2.motif 0.0152125
Elf4	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00566999	Pattern Name Homer Significance motif2.motif 0.00895127
Elk3	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00397752 metacluster_1/pattern_6 0.0248876	Pattern Name Homer Significance motif2.motif 0.0007655639999999999
Spdef	Pattern Name Modisco Significance metacluster_1/pattern_2 0.043557099999999994	Pattern Name Homer Significance motif2.motif 0.0421949
Etv5	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00483995 metacluster_1/pattern_6 0.018559299999999997	Pattern Name Homer Significance motif2.motif 0.00022113900000000003
Etv2	Pattern Name Modisco Significance metacluster_1/pattern_2 7.060310000000001e-05 metacluster_1/pattern_6 0.018559299999999997	Pattern Name Homer Significance motif2.motif 0.00147568
Zfp143	Pattern Name Modisco Significance metacluster_1/pattern_5 7.50483e-09	Pattern Name Homer Significance motif7.motif 1.02649e-06
Elf1	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00106377	Pattern Name Homer Significance motif2.motif 0.0008750380000000001
XP_911724.4	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00355199	Pattern Name Homer Significance motif2.motif 0.0008750380000000001
Ehf	Pattern Name Modisco Significance metacluster_1/pattern_2 0.0303231 metacluster_1/pattern_6 0.050570699999999996	Pattern Name Homer Significance motif2.motif 0.028776299999999998
Elk4	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00355199 metacluster_1/pattern_6 0.0583058	Pattern Name Homer Significance motif2.motif 0.000517533
Elf2	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00986639 metacluster_1/pattern_6 0.018559299999999997	Pattern Name Homer Significance motif2.motif 0.0160288
Irf7	Pattern Name Modisco Significance metacluster_1/pattern_3 4.3180200000000004e-05	Pattern Name Homer Significance motif6.motif 0.039390100000000004
Ctcfl	Pattern Name Modisco Significance metacluster_1/pattern_0 4.974060000000001e-07 metacluster_1/pattern_1 0.057135000000000005	Pattern Name Homer Significance motif1.motif 0.000189028
Elf3	Pattern Name Modisco Significance metacluster_1/pattern_2 0.022549200000000002	Pattern Name Homer Significance motif2.motif 0.0566915
Gabpa	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00513367 metacluster_1/pattern_6 0.0407209	Pattern Name Homer Significance motif2.motif 0.00082812
Ets1	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00257166 metacluster_1/pattern_6 0.0456245	Pattern Name Homer Significance motif2.motif 0.0007655639999999999
Irf9	Pattern Name Modisco Significance metacluster_1/pattern_3 0.00223351	Pattern Name Homer Significance motif6.motif 0.0216638
Tbx2	Pattern Name Modisco Significance metacluster_1/pattern_5 7.50483e-09	Pattern Name Homer Significance motif7.motif 6.73135e-05
Spi1	Pattern Name Modisco Significance metacluster_1/pattern_2 0.0370544 metacluster_1/pattern_6 0.0381566	Pattern Name Homer Significance motif2.motif 0.0186041
Ctcf	Pattern Name Modisco Significance metacluster_1/pattern_0 2.09254e-14 metacluster_1/pattern_1 0.00293923	Pattern Name Homer Significance motif1.motif 4.923569999999999e-06

Unique TF-MoDISco TFs: #25

TF Name	Modisco	Homer
Irf8	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00355199 metacluster_1/pattern_3 4.3180200000000004e-05	Absent
Spib	Pattern Name Modisco Significance metacluster_1/pattern_2 0.000644258 metacluster_1/pattern_3 0.00236355	Absent
Fosb	Pattern Name Modisco Significance metacluster_1/pattern_4 0.00155978 metacluster_1/pattern_6 0.018559299999999997	Absent
Rest	Pattern Name Modisco Significance metacluster_1/pattern_7 1.51099e-14	Absent
Jund	Pattern Name Modisco Significance metacluster_1/pattern_4 0.00394352 metacluster_1/pattern_6 0.0248876	Absent
Bach2	Pattern Name Modisco Significance metacluster_1/pattern_4 0.020729499999999998	Absent
T	Pattern Name Modisco Significance metacluster_1/pattern_6 0.018559299999999997	Absent
Spic	Pattern Name Modisco Significance metacluster_1/pattern_2 0.00790418	Absent
Rorc	Pattern Name Modisco Significance metacluster_1/pattern_6 0.0248876	Absent
Stat2	Pattern Name Modisco Significance metacluster_1/pattern_3 6.40394e-05	Absent
Fosl2	Pattern Name Modisco Significance metacluster_1/pattern_4 0.00626675 metacluster_1/pattern_6 0.018559299999999997	Absent
Batf3	Pattern Name Modisco Significance metacluster_1/pattern_3 0.0360824 metacluster_1/pattern_4 0.00189355	Absent
Atf3	Pattern Name Modisco Significance metacluster_1/pattern_4 0.00218776 metacluster_1/pattern_6 0.0220298	Absent
Fos	Pattern Name Modisco Significance metacluster_1/pattern_4 0.00209698 metacluster_1/pattern_6 0.0381566	Absent
Nfe2l2	Pattern Name Modisco Significance metacluster_1/pattern_4 0.00686171	Absent
Stat3	Pattern Name Modisco Significance metacluster_1/pattern_5 0.028527499999999997	Absent
Fosl1	Pattern Name Modisco Significance metacluster_1/pattern_4 0.00344027 metacluster_1/pattern_6 0.0381566	Absent
Prdm1	Pattern Name Modisco Significance metacluster_1/pattern_2 0.0145505 metacluster_1/pattern_3 0.000446728	Absent
Nfatc1	Pattern Name Modisco Significance metacluster_1/pattern_4 0.051769	Absent
Jun	Pattern Name Modisco Significance metacluster_1/pattern_4 0.058202 metacluster_1/pattern_6 0.0178092	Absent
Stat1	Pattern Name Modisco Significance metacluster_1/pattern_3 2.8692e-06	Absent
Jdp2	Pattern Name Modisco Significance metacluster_1/pattern_4 4.6230599999999996e-06 metacluster_1/pattern_6 0.018559299999999997	Absent
Irf1	Pattern Name Modisco Significance metacluster_1/pattern_3 5.9939e-09	Absent
Junb	Pattern Name Modisco Significance metacluster_1/pattern_4 0.017496400000000002 metacluster_1/pattern_6 0.030546499999999997	Absent
Batf	Pattern Name Modisco Significance metacluster_1/pattern_4 0.00017937099999999997 metacluster_1/pattern_6 0.0178092	Absent

Unique Homer TFs: #40

TF Name	Modisco	Homer
Klf3	Absent	Pattern Name Homer Significance motif3.motif 0.00034182
Zfp42	Absent	Pattern Name Homer Significance motif14.motif 0.025294099999999996
E2f4	Absent	Pattern Name Homer Significance motif3.motif 0.00048016800000000006
Yy1	Absent	Pattern Name Homer Significance motif14.motif 3.51526e-05
Rela	Absent	Pattern Name Homer Significance motif18.motif 0.000542213
Zfp281	Absent	Pattern Name Homer Significance motif3.motif 0.053991
Nfya	Absent	Pattern Name Homer Significance motif9.motif 2.95166e-06
Klf5	Absent	Pattern Name Homer Significance motif3.motif 0.00870626
Nfyc	Absent	Pattern Name Homer Significance motif9.motif 5.81558e-06
Pbx3	Absent	Pattern Name Homer Significance motif9.motif 0.000396653
Egr1	Absent	Pattern Name Homer Significance motif3.motif 0.047002300000000004
Taf1	Absent	Pattern Name Homer Significance motif14.motif 0.00051887
Egr2	Absent	Pattern Name Homer Significance motif3.motif 0.036674599999999995
Irf5	Absent	Pattern Name Homer Significance motif6.motif 0.030336099999999998
Klf7	Absent	Pattern Name Homer Significance motif3.motif 0.000362306
Klf12	Absent	Pattern Name Homer Significance motif3.motif 0.0325621
Sp2	Absent	Pattern Name Homer Significance motif3.motif 0.000124698
Zbtb1	Absent	Pattern Name Homer Significance motif3.motif 0.0137376
Klf1	Absent	Pattern Name Homer Significance motif3.motif 0.047002300000000004
E2f7	Absent	Pattern Name Homer Significance motif3.motif 0.00942314
Nrf1	Absent	Pattern Name Homer Significance motif10.motif 1.85491e-07
Relb	Absent	Pattern Name Homer Significance motif18.motif 0.00178309
Runx3	Absent	Pattern Name Homer Significance motif12.motif 0.0337742
E2f6	Absent	Pattern Name Homer Significance motif3.motif 0.016942099999999998
Klf6	Absent	Pattern Name Homer Significance motif3.motif 0.00221498
E2f1	Absent	Pattern Name Homer Significance motif3.motif 0.00469127
Klf15	Absent	Pattern Name Homer Significance motif3.motif 0.00942314
Sp4	Absent	Pattern Name Homer Significance motif3.motif 0.00677345
Zbtb17	Absent	Pattern Name Homer Significance motif3.motif 0.00317956
Sp1	Absent	Pattern Name Homer Significance motif3.motif 0.0028425
Sp5	Absent	Pattern Name Homer Significance motif3.motif 0.036674599999999995
Foxi1	Absent	Pattern Name Homer Significance motif9.motif 0.00133412
Nfkb2	Absent	Pattern Name Homer Significance motif18.motif 0.00037016
Nfyb	Absent	Pattern Name Homer Significance motif9.motif 4.92437e-08
Klf8	Absent	Pattern Name Homer Significance motif3.motif 0.00057705
Nfkb1	Absent	Pattern Name Homer Significance motif18.motif 8.70161e-05
Klf4	Absent	Pattern Name Homer Significance motif3.motif 0.0248979
Sp3	Absent	Pattern Name Homer Significance motif3.motif 0.000124698
Runx1	Absent	Pattern Name Homer Significance motif12.motif 0.0337742
Cbfb	Absent	Pattern Name Homer Significance motif12.motif 0.0451068