# Parameters
data_name = "immatureB_SPLND;CD43-_CD11b-;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_210-naivegw"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_210-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 19:28:21,512 [WARNING] git-lfs not installed

display_metadata(data_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	mouse spleen B cells, CD43-,CD11b- (immature B cells)
Cell Group	B 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	125656	99407	7.0454	180941018	NA	NA	NA	NA	NA	NA

Modelling Metadata

Metric	Value
auPRC	0.6158
Calibrated Recall at 50% FDR	0.217
Number of Positive Examples in Test Data	84892
Number of Negative Examples in Test Data	7985959
Imbalance Ratio in Test Data	0.0105
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: 11825 SequenceContrib ScoresHyp_Contrib Scores	Ctcf, Ctcfl
metacluster_1/pattern_1 # seqlets: 1459 SequenceContrib ScoresHyp_Contrib Scores	Spi1, Spib, Irf8, Irf4, Prdm1, Elf3, Spic, Irf3, Ehf, Etv2, Ets1, Irf2, Irf1, Elf5, Gabpa, Elf1, Erg, Etv6, Etv4, Elk1, Elf4, Etv3, Elf2, Fli1, XP_911724.4, Bcl6
metacluster_1/pattern_2 # seqlets: 893 SequenceContrib ScoresHyp_Contrib Scores
metacluster_1/pattern_3 # seqlets: 861 SequenceContrib ScoresHyp_Contrib Scores	Stat2, Zscan10, Irf7, Irf9, Stat1
metacluster_1/pattern_4 # seqlets: 411 SequenceContrib ScoresHyp_Contrib Scores	Zfp143, Thap11, Tbx2
metacluster_1/pattern_5 # seqlets: 39 SequenceContrib ScoresHyp_Contrib Scores	Nrf1, Sp2, Sp3, Klf3, Trp53, Zfx, Sp1
metacluster_1/pattern_6 # seqlets: 33 SequenceContrib ScoresHyp_Contrib Scores	Rfx1, Rfx3, Rfx2, Rfx4, Rfx7, Rfx6
metacluster_1/pattern_7 # seqlets: 57 SequenceContrib ScoresHyp_Contrib Scores	Usf2, Elk4, Etv1, Creb1, Elk3, Etv5, Fev, Atf1, Atf2, Atf7, Crem

Click here for Motifs by TF-MoDISco: #60

TF Name	Pattern(s)
Ctcf	Pattern Name Modisco Significance metacluster_1/pattern_0 2.57772e-15 metacluster_1/pattern_2 0.00419748
Ctcfl	Pattern Name Modisco Significance metacluster_1/pattern_0 3.06874e-07 metacluster_1/pattern_2 0.051682500000000006
Spi1	Pattern Name Modisco Significance metacluster_1/pattern_1 0.00140627 metacluster_1/pattern_3 0.0060034
Spib	Pattern Name Modisco Significance metacluster_1/pattern_1 5.977530000000001e-10 metacluster_1/pattern_3 5.21979e-07
Irf8	Pattern Name Modisco Significance metacluster_1/pattern_1 7.37669e-07 metacluster_1/pattern_3 4.5965699999999997e-14
Irf4	Pattern Name Modisco Significance metacluster_1/pattern_1 1.3677500000000002e-06 metacluster_1/pattern_3 0.0481952
Prdm1	Pattern Name Modisco Significance metacluster_1/pattern_1 0.00037988199999999995 metacluster_1/pattern_3 0.00817878
Elf3	Pattern Name Modisco Significance metacluster_1/pattern_1 0.039593500000000004
Spic	Pattern Name Modisco Significance metacluster_1/pattern_1 0.00442074 metacluster_1/pattern_3 0.0491048
Irf3	Pattern Name Modisco Significance metacluster_1/pattern_1 0.000728658 metacluster_1/pattern_3 0.00212942
Ehf	Pattern Name Modisco Significance metacluster_1/pattern_1 0.0008959430000000001
Etv2	Pattern Name Modisco Significance metacluster_1/pattern_1 0.00103638
Ets1	Pattern Name Modisco Significance metacluster_1/pattern_1 0.039267800000000005 metacluster_1/pattern_7 0.0347686
Irf2	Pattern Name Modisco Significance metacluster_1/pattern_1 0.00224878 metacluster_1/pattern_3 0.043151
Irf1	Pattern Name Modisco Significance metacluster_1/pattern_1 0.00320247 metacluster_1/pattern_3 4.81017e-05
Elf5	Pattern Name Modisco Significance metacluster_1/pattern_1 0.051592700000000005
Gabpa	Pattern Name Modisco Significance metacluster_1/pattern_1 0.0431615 metacluster_1/pattern_7 0.0205861
Elf1	Pattern Name Modisco Significance metacluster_1/pattern_1 0.00904088 metacluster_1/pattern_7 0.014602799999999999
Erg	Pattern Name Modisco Significance metacluster_1/pattern_1 0.043825499999999996 metacluster_1/pattern_7 0.026714599999999995
Etv6	Pattern Name Modisco Significance metacluster_1/pattern_1 0.023893
Etv4	Pattern Name Modisco Significance metacluster_1/pattern_1 0.0180588 metacluster_1/pattern_7 0.020133900000000003
Elk1	Pattern Name Modisco Significance metacluster_1/pattern_1 0.045883600000000004 metacluster_1/pattern_7 0.0172563
Elf4	Pattern Name Modisco Significance metacluster_1/pattern_1 0.0335649
Etv3	Pattern Name Modisco Significance metacluster_1/pattern_1 0.039267800000000005
Elf2	Pattern Name Modisco Significance metacluster_1/pattern_1 0.0508199
Fli1	Pattern Name Modisco Significance metacluster_1/pattern_1 0.051592700000000005 metacluster_1/pattern_7 0.033017000000000005
XP_911724.4	Pattern Name Modisco Significance metacluster_1/pattern_1 0.043825499999999996
Bcl6	Pattern Name Modisco Significance metacluster_1/pattern_1 0.0508199
Stat2	Pattern Name Modisco Significance metacluster_1/pattern_3 0.00701224
Zscan10	Pattern Name Modisco Significance metacluster_1/pattern_3 0.00893613
Irf7	Pattern Name Modisco Significance metacluster_1/pattern_3 0.00902612
Irf9	Pattern Name Modisco Significance metacluster_1/pattern_3 0.016780200000000002
Stat1	Pattern Name Modisco Significance metacluster_1/pattern_3 0.018491099999999996
Zfp143	Pattern Name Modisco Significance metacluster_1/pattern_4 3.9730399999999997e-19
Thap11	Pattern Name Modisco Significance metacluster_1/pattern_4 1.8293599999999996e-18
Tbx2	Pattern Name Modisco Significance metacluster_1/pattern_4 1.77113e-13
Nrf1	Pattern Name Modisco Significance metacluster_1/pattern_5 9.061260000000001e-05
Sp2	Pattern Name Modisco Significance metacluster_1/pattern_5 0.00933334 metacluster_1/pattern_7 0.00480167
Sp3	Pattern Name Modisco Significance metacluster_1/pattern_5 0.026040300000000002 metacluster_1/pattern_7 0.00748667
Klf3	Pattern Name Modisco Significance metacluster_1/pattern_5 0.0359087
Trp53	Pattern Name Modisco Significance metacluster_1/pattern_5 0.057483000000000006
Zfx	Pattern Name Modisco Significance metacluster_1/pattern_5 0.057483000000000006 metacluster_1/pattern_7 0.00752257
Sp1	Pattern Name Modisco Significance metacluster_1/pattern_5 0.057483000000000006 metacluster_1/pattern_7 0.020701400000000002
Rfx1	Pattern Name Modisco Significance metacluster_1/pattern_6 5.15369e-05
Rfx3	Pattern Name Modisco Significance metacluster_1/pattern_6 0.029669099999999997
Rfx2	Pattern Name Modisco Significance metacluster_1/pattern_6 2.66701e-07
Rfx4	Pattern Name Modisco Significance metacluster_1/pattern_6 0.000788975
Rfx7	Pattern Name Modisco Significance metacluster_1/pattern_6 0.00900075
Rfx6	Pattern Name Modisco Significance metacluster_1/pattern_6 0.00437395
Usf2	Pattern Name Modisco Significance metacluster_1/pattern_7 0.00294219
Elk4	Pattern Name Modisco Significance metacluster_1/pattern_7 0.0241391
Etv1	Pattern Name Modisco Significance metacluster_1/pattern_7 0.00661023
Creb1	Pattern Name Modisco Significance metacluster_1/pattern_7 0.020701400000000002
Elk3	Pattern Name Modisco Significance metacluster_1/pattern_7 0.00684215
Etv5	Pattern Name Modisco Significance metacluster_1/pattern_7 0.00661023
Fev	Pattern Name Modisco Significance metacluster_1/pattern_7 0.00684215
Atf1	Pattern Name Modisco Significance metacluster_1/pattern_7 0.00715435
Atf2	Pattern Name Modisco Significance metacluster_1/pattern_7 0.026714599999999995
Atf7	Pattern Name Modisco Significance metacluster_1/pattern_7 0.046692199999999996
Crem	Pattern Name Modisco Significance metacluster_1/pattern_7 0.0486329

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: #48

TF Name	Modisco	Homer
XP_911724.4	Pattern Name Modisco Significance metacluster_1/pattern_1 0.043825499999999996	Pattern Name Homer Significance motif3.motif 0.000169657
Elf1	Pattern Name Modisco Significance metacluster_1/pattern_1 0.00904088 metacluster_1/pattern_7 0.014602799999999999	Pattern Name Homer Significance motif3.motif 6.58593e-05
Prdm1	Pattern Name Modisco Significance metacluster_1/pattern_1 0.00037988199999999995 metacluster_1/pattern_3 0.00817878	Pattern Name Homer Significance motif3.motif 0.015265299999999999 motif11.motif 0.00890098
Elf2	Pattern Name Modisco Significance metacluster_1/pattern_1 0.0508199	Pattern Name Homer Significance motif3.motif 0.037856400000000005
Stat1	Pattern Name Modisco Significance metacluster_1/pattern_3 0.018491099999999996	Pattern Name Homer Significance motif11.motif 0.0522766
Irf4	Pattern Name Modisco Significance metacluster_1/pattern_1 1.3677500000000002e-06 metacluster_1/pattern_3 0.0481952	Pattern Name Homer Significance motif3.motif 0.00155049 motif11.motif 0.00316696
Sp2	Pattern Name Modisco Significance metacluster_1/pattern_5 0.00933334 metacluster_1/pattern_7 0.00480167	Pattern Name Homer Significance motif2.motif 0.000427125
Fev	Pattern Name Modisco Significance metacluster_1/pattern_7 0.00684215	Pattern Name Homer Significance motif3.motif 0.000646821
Ctcfl	Pattern Name Modisco Significance metacluster_1/pattern_0 3.06874e-07 metacluster_1/pattern_2 0.051682500000000006	Pattern Name Homer Significance motif1.motif 4.6891499999999996e-05
Etv6	Pattern Name Modisco Significance metacluster_1/pattern_1 0.023893	Pattern Name Homer Significance motif3.motif 0.00700372
Klf3	Pattern Name Modisco Significance metacluster_1/pattern_5 0.0359087	Pattern Name Homer Significance motif2.motif 0.000427035
Spi1	Pattern Name Modisco Significance metacluster_1/pattern_1 0.00140627 metacluster_1/pattern_3 0.0060034	Pattern Name Homer Significance motif3.motif 0.00241045
Creb1	Pattern Name Modisco Significance metacluster_1/pattern_7 0.020701400000000002	Pattern Name Homer Significance motif15.motif 0.0380614
Etv3	Pattern Name Modisco Significance metacluster_1/pattern_1 0.039267800000000005	Pattern Name Homer Significance motif3.motif 0.000169657
Elk3	Pattern Name Modisco Significance metacluster_1/pattern_7 0.00684215	Pattern Name Homer Significance motif3.motif 0.000169657
Erg	Pattern Name Modisco Significance metacluster_1/pattern_1 0.043825499999999996 metacluster_1/pattern_7 0.026714599999999995	Pattern Name Homer Significance motif3.motif 6.58593e-05
Crem	Pattern Name Modisco Significance metacluster_1/pattern_7 0.0486329	Pattern Name Homer Significance motif15.motif 0.0380614
Sp3	Pattern Name Modisco Significance metacluster_1/pattern_5 0.026040300000000002 metacluster_1/pattern_7 0.00748667	Pattern Name Homer Significance motif2.motif 0.000427035
Atf1	Pattern Name Modisco Significance metacluster_1/pattern_7 0.00715435	Pattern Name Homer Significance motif15.motif 0.045450800000000006
Irf1	Pattern Name Modisco Significance metacluster_1/pattern_1 0.00320247 metacluster_1/pattern_3 4.81017e-05	Pattern Name Homer Significance motif3.motif 0.0322095 motif11.motif 0.000782635
Stat2	Pattern Name Modisco Significance metacluster_1/pattern_3 0.00701224	Pattern Name Homer Significance motif11.motif 0.0159467
Etv2	Pattern Name Modisco Significance metacluster_1/pattern_1 0.00103638	Pattern Name Homer Significance motif3.motif 0.00020083200000000002
Spib	Pattern Name Modisco Significance metacluster_1/pattern_1 5.977530000000001e-10 metacluster_1/pattern_3 5.21979e-07	Pattern Name Homer Significance motif3.motif 0.000206299 motif11.motif 0.0129755
Elk4	Pattern Name Modisco Significance metacluster_1/pattern_7 0.0241391	Pattern Name Homer Significance motif3.motif 6.58593e-05
Irf8	Pattern Name Modisco Significance metacluster_1/pattern_1 7.37669e-07 metacluster_1/pattern_3 4.5965699999999997e-14	Pattern Name Homer Significance motif3.motif 0.00133733 motif11.motif 0.000782635
Elf4	Pattern Name Modisco Significance metacluster_1/pattern_1 0.0335649	Pattern Name Homer Significance motif3.motif 0.000964342
Fli1	Pattern Name Modisco Significance metacluster_1/pattern_1 0.051592700000000005 metacluster_1/pattern_7 0.033017000000000005	Pattern Name Homer Significance motif3.motif 6.58593e-05
Etv1	Pattern Name Modisco Significance metacluster_1/pattern_7 0.00661023	Pattern Name Homer Significance motif3.motif 0.00012161299999999999
Thap11	Pattern Name Modisco Significance metacluster_1/pattern_4 1.8293599999999996e-18	Pattern Name Homer Significance motif5.motif 2.96253e-07
Nrf1	Pattern Name Modisco Significance metacluster_1/pattern_5 9.061260000000001e-05	Pattern Name Homer Significance motif6.motif 0.00143337
Ets1	Pattern Name Modisco Significance metacluster_1/pattern_1 0.039267800000000005 metacluster_1/pattern_7 0.0347686	Pattern Name Homer Significance motif3.motif 6.58593e-05
Elk1	Pattern Name Modisco Significance metacluster_1/pattern_1 0.045883600000000004 metacluster_1/pattern_7 0.0172563	Pattern Name Homer Significance motif3.motif 6.58593e-05
Elf3	Pattern Name Modisco Significance metacluster_1/pattern_1 0.039593500000000004	Pattern Name Homer Significance motif3.motif 0.00938877
Tbx2	Pattern Name Modisco Significance metacluster_1/pattern_4 1.77113e-13	Pattern Name Homer Significance motif5.motif 5.184399999999999e-07
Irf2	Pattern Name Modisco Significance metacluster_1/pattern_1 0.00224878 metacluster_1/pattern_3 0.043151	Pattern Name Homer Significance motif3.motif 0.020703299999999997 motif11.motif 0.00205606
Irf7	Pattern Name Modisco Significance metacluster_1/pattern_3 0.00902612	Pattern Name Homer Significance motif11.motif 0.0101635
Atf2	Pattern Name Modisco Significance metacluster_1/pattern_7 0.026714599999999995	Pattern Name Homer Significance motif15.motif 0.0380614
Atf7	Pattern Name Modisco Significance metacluster_1/pattern_7 0.046692199999999996	Pattern Name Homer Significance motif15.motif 0.0380614
Etv4	Pattern Name Modisco Significance metacluster_1/pattern_1 0.0180588 metacluster_1/pattern_7 0.020133900000000003	Pattern Name Homer Significance motif3.motif 0.00157346
Irf3	Pattern Name Modisco Significance metacluster_1/pattern_1 0.000728658 metacluster_1/pattern_3 0.00212942	Pattern Name Homer Significance motif3.motif 0.0476619
Gabpa	Pattern Name Modisco Significance metacluster_1/pattern_1 0.0431615 metacluster_1/pattern_7 0.0205861	Pattern Name Homer Significance motif3.motif 0.000851506
Sp1	Pattern Name Modisco Significance metacluster_1/pattern_5 0.057483000000000006 metacluster_1/pattern_7 0.020701400000000002	Pattern Name Homer Significance motif2.motif 0.00928863
Elf5	Pattern Name Modisco Significance metacluster_1/pattern_1 0.051592700000000005	Pattern Name Homer Significance motif3.motif 0.0452055
Etv5	Pattern Name Modisco Significance metacluster_1/pattern_7 0.00661023	Pattern Name Homer Significance motif3.motif 0.000169657
Ctcf	Pattern Name Modisco Significance metacluster_1/pattern_0 2.57772e-15 metacluster_1/pattern_2 0.00419748	Pattern Name Homer Significance motif1.motif 7.38343e-08
Ehf	Pattern Name Modisco Significance metacluster_1/pattern_1 0.0008959430000000001	Pattern Name Homer Significance motif3.motif 0.00381713
Spic	Pattern Name Modisco Significance metacluster_1/pattern_1 0.00442074 metacluster_1/pattern_3 0.0491048	Pattern Name Homer Significance motif3.motif 0.00297662
Zfp143	Pattern Name Modisco Significance metacluster_1/pattern_4 3.9730399999999997e-19	Pattern Name Homer Significance motif5.motif 2.96253e-07

Unique TF-MoDISco TFs: #12

TF Name	Modisco	Homer
Trp53	Pattern Name Modisco Significance metacluster_1/pattern_5 0.057483000000000006	Absent
Rfx2	Pattern Name Modisco Significance metacluster_1/pattern_6 2.66701e-07	Absent
Bcl6	Pattern Name Modisco Significance metacluster_1/pattern_1 0.0508199	Absent
Usf2	Pattern Name Modisco Significance metacluster_1/pattern_7 0.00294219	Absent
Rfx4	Pattern Name Modisco Significance metacluster_1/pattern_6 0.000788975	Absent
Rfx1	Pattern Name Modisco Significance metacluster_1/pattern_6 5.15369e-05	Absent
Rfx3	Pattern Name Modisco Significance metacluster_1/pattern_6 0.029669099999999997	Absent
Rfx7	Pattern Name Modisco Significance metacluster_1/pattern_6 0.00900075	Absent
Rfx6	Pattern Name Modisco Significance metacluster_1/pattern_6 0.00437395	Absent
Zfx	Pattern Name Modisco Significance metacluster_1/pattern_5 0.057483000000000006 metacluster_1/pattern_7 0.00752257	Absent
Zscan10	Pattern Name Modisco Significance metacluster_1/pattern_3 0.00893613	Absent
Irf9	Pattern Name Modisco Significance metacluster_1/pattern_3 0.016780200000000002	Absent

Unique Homer TFs: #29

TF Name	Modisco	Homer
Rela	Absent	Pattern Name Homer Significance motif21.motif 0.0012963
Spdef	Absent	Pattern Name Homer Significance motif3.motif 0.015265299999999999
Foxi1	Absent	Pattern Name Homer Significance motif7.motif 0.00096093
Klf6	Absent	Pattern Name Homer Significance motif2.motif 0.00423613
Snai1	Absent	Pattern Name Homer Significance motif1.motif 0.0503809
Egr1	Absent	Pattern Name Homer Significance motif2.motif 0.018080799999999998
Klf7	Absent	Pattern Name Homer Significance motif2.motif 0.000427125
Klf1	Absent	Pattern Name Homer Significance motif2.motif 0.040231
E2f4	Absent	Pattern Name Homer Significance motif2.motif 0.00126624
Klf8	Absent	Pattern Name Homer Significance motif2.motif 0.0009202739999999999
Relb	Absent	Pattern Name Homer Significance motif21.motif 0.00370558
Zbtb1	Absent	Pattern Name Homer Significance motif2.motif 0.051469900000000006
Yy1	Absent	Pattern Name Homer Significance motif16.motif 1.07651e-06
Zfp42	Absent	Pattern Name Homer Significance motif16.motif 0.00047637900000000003
Nfyb	Absent	Pattern Name Homer Significance motif7.motif 1.04471e-06
Klf5	Absent	Pattern Name Homer Significance motif2.motif 0.025638099999999997
Rel	Absent	Pattern Name Homer Significance motif21.motif 0.010101899999999999
Taf1	Absent	Pattern Name Homer Significance motif16.motif 2.99143e-05
Klf4	Absent	Pattern Name Homer Significance motif2.motif 0.000463374
Zic2	Absent	Pattern Name Homer Significance motif1.motif 0.0336453
Nfyc	Absent	Pattern Name Homer Significance motif7.motif 1.5457e-05
Nfya	Absent	Pattern Name Homer Significance motif7.motif 9.14635e-06
Sp4	Absent	Pattern Name Homer Significance motif2.motif 0.019171200000000003
Nfkb1	Absent	Pattern Name Homer Significance motif21.motif 0.000112727
Pbx3	Absent	Pattern Name Homer Significance motif7.motif 0.000875804
Klf12	Absent	Pattern Name Homer Significance motif2.motif 0.014141599999999999
Nfkb2	Absent	Pattern Name Homer Significance motif21.motif 0.000112727
Mafb	Absent	Pattern Name Homer Significance motif15.motif 0.045450800000000006
Zic3	Absent	Pattern Name Homer Significance motif1.motif 0.0336453