In [1]:
# Parameters
data_name = "Smarcc2"
task_idxs = "0-213,216-278"
homer_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_scans"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
In [2]:
from matlas.modisco_report import call_motifDB_to_be_displayed, display_comparative_cell_types
load data from labcluster
Using TensorFlow backend.
2019-07-26 02:02:04,344 [WARNING] git-lfs not installed
In [3]:
homer_matches, modisco_matches = call_motifDB_to_be_displayed(task_idxs, homer_root, modisco_root)
In [4]:
display_comparative_cell_types(data_name, homer_matches, modisco_matches)
TF-MoDISco is using the TensorFlow backend.

CISBP ID of Smarcc2: M4527_1.02

Shared Cell types both TF-MoDISco and Homer finds Smarcc2
Cell typeModiscoHomer
memory TCR SV40-I CD8 T cells isolated D7 from established tumors (with listeria immunization)

Significance: 4.25975e-17

Significance: 2.68994e-06

memory TCR SV40-I CD8 T cells isolated D14 from established tumors (with listeria immunization)

Significance: 1.6011700000000002e-17

Significance: 9.133839999999998e-06

memory TCR SV40-I CD8 T cells isolated D7 from established tumors (without listeria immunization)

Significance: 1.01037e-17

Significance: 5.08921e-07

immature B cells

Significance: 1.00435e-20

Significance: 6.46565e-07

Act B cell

Significance: 4.5883400000000003e-17

Significance: 3.8227200000000005e-07

Pre-PB

Significance: 1.8049799999999998e-17

Significance: 8.249700000000002e-07

GC B cells

Significance: 7.28096e-18

Significance: 1.04349e-07

plasma cells

Significance: 2.11821e-16

Significance: 1.2579299999999998e-06

skeletal muscle tissue(adult-8wks)

Significance: 3.9942300000000004e-16

Significance: 1.19134e-06

bone marrow-derived macrophages(Lipid A stimulation 120min)

Significance: 8.25135e-18

Significance: 8.176649999999999e-07

aB LPS+a-d-dextran

Significance: 6.6143e-19

Significance: 1.4085399999999998e-06

Ter119+ Erythroid cells

Significance: 4.8613800000000007e-20

Significance: 5.2101e-07

CH12.LX cell line

Significance: 1.12783e-17

Significance: 1.09463e-07

ES_derived Definitive Endoderm

Significance: 3.64104e-16

Significance: 0.0222891

Significance: 3.94399e-07

Tfh (CD4+CD44+CXCR5+PD1+CD25-) Mut

Significance: 7.840269999999999e-14

Significance: 4.57385e-07

activated non-Tfh (CD4+CD44+CXCR5-PD1-CD25-) WT

Significance: 9.719589999999999e-18

Significance: 6.70343e-07

embryo_3rd rhombomere (E8.5, deltaA)

Significance: 4.652129999999999e-15

Significance: 1.67047e-07

Tfr (CD4+CD44+CXCR5+PD1+CD25+) WT

Significance: 5.89106e-18

Significance: 5.013920000000001e-07

CD4+CD8+ CD69lo small (DP precursors)

Significance: 1.69707e-17

Significance: 4.56462e-06

CD4+CD8int TCRhi CD69hi CD24hi (B2m def mice)

Significance: 5.29857e-19

Significance: 2.18103e-07

CD4+CD8int TCRhi CD69hi CD24hi (MHCII def mice)

Significance: 8.92484e-18

Significance: 1.08997e-05

CD4-CD8+ TCRhi CD69hi CD24hi (MHCII def mice)

Significance: 4.97929e-17

Significance: 2.62523e-06

CD4-CD8+ TCRhi CD69lo CD24lo (MHCII def mice)

Significance: 6.134730000000001e-18

Significance: 2.72395e-06

neural progenitor cells(G4)

Significance: 1.53497e-15

Significance: 4.4625399999999997e-07

macrophage

Significance: 1.4649999999999998e-17

Significance: 2.29279e-07

Erythroblasts

Significance: 1.0722500000000001e-19

Significance: 4.96781e-07

DN3a

Significance: 1.4539000000000003e-17

Significance: 3.4038300000000003e-06

ISP (Immature single positive)

Significance: 1.6600299999999998e-18

Significance: 3.0720400000000002e-06

Cortical excitatory neurons

Significance: 6.66258e-16

Significance: 2.1556599999999999e-07

MEFs

Significance: 4.78641e-16

Significance: 8.51926e-08

BptfKO Mammary Cells

Significance: 2.82647e-15

Significance: 2.32996e-07

NCR+ILC3+IL23

Significance: 3.8249e-17

Significance: 4.47243e-06

Th2 (Nippo infected)

Significance: 5.79655e-17

Significance: 2.55248e-07

Fibroblast/NIH3T3

Significance: 2.19171e-16

Significance: 1.22135e-06

Fibroblast (adult-8wks)

Significance: 1.7209e-16

Significance: 3.6617400000000003e-06

naive transgenic TCR SV40-I CD8 T cells

Significance: 1.4249999999999997e-17

Significance: 4.37522e-06

Spleen CD8+ T cell(MPEC)

Significance: 9.361110000000001e-18

Significance: 1.3808600000000002e-06

Heart (adult-8wks)

Significance: 5.06174e-17

Significance: 2.0372e-06

heart tissue(P0)

Significance: 4.07468e-17

Significance: 2.8551599999999995e-06

Retina(newborn 1 day)

Significance: 1.50355e-12

Significance: 7.18332e-08

mixed embryonic mouse retina(E14.5)

Significance: 4.30059e-15

Significance: 1.99662e-06

ILC3(WT)

Significance: 8.23727e-18

Significance: 2.7553400000000004e-08

Activated primary T regulatory cells(adult-8wks)

Significance: 1.2255799999999999e-17

Significance: 9.691560000000001e-08

Naive CD8+ T cell

Significance: 7.34596e-18

Significance: 4.0893e-06

Muller cell(P12)

Significance: 1.36335e-14

Significance: 1.34938e-08

Spleen CD8+ T cell (Exhausted)

Significance: 5.57903e-18

Significance: 1.55496e-07

Spleen CD8+ T cell(SLEC)

Significance: 5.2862e-19

Significance: 5.909780000000001e-06

mixed embryonic mouse hindbrain(E11.5)

Significance: 1.50415e-15

Significance: 3.3183e-07

D7 effector TCR SV40-I CD8 T cells

Significance: 4.8535300000000004e-18

Significance: 3.07329e-06

TCR SV40-I CD8 T cells isolated D5 from early malignant lesions

Significance: 4.9858800000000005e-17

Significance: 6.43427e-07

TCR SV40-I CD8 T cells isolated D14 from early malignant lesions

Significance: 1.90587e-17

Significance: 1.10043e-07

Unique Cell types only TF-MoDISco finds Smarcc2
Cell typeModiscoHomer
MPP

Significance: 4.6293099999999994e-18

absent
naive CD8

Significance: 8.54026e-17

absent
CD25CCR6 DN CD4 (memory CD4+ T cell)

Significance: 3.40709e-17

absent
Th17 CD4

Significance: 2.70065e-17

absent
NK cells (spleen)

Significance: 3.0560400000000006e-18

absent
proB cells

Significance: 4.2329500000000003e-19

absent
preB cells

Significance: 1.78e-19

absent
mature B cells

Significance: 6.89198e-19

absent
MZ B cells

Significance: 9.70907e-16

absent
B1 B cells

Significance: 2.49875e-19

absent
aB LPS

Significance: 6.079130000000001e-19

absent
aB LPS+IL4

Significance: 3.3986199999999993e-18

absent
aB LPS+IL21

Significance: 2.0924599999999997e-18

absent
aB aCD40+IL4

Significance: 2.28135e-18

absent
mast cells

Significance: 3.85873e-17

absent
basophils

Significance: 3.99983e-18

absent
eosinphils (ex-vivo, BalbC)

Significance: 8.597189999999999e-19

absent
eosinophils (isolated from spleens, BalbC)

Significance: 5.42529e-18

absent
neutrophils

Significance: 6.039590000000001e-18

absent
Tfh from infected with LCMV

Significance: 9.59021e-19

absent
Tfh (CD4+CD44+CXCR5+PD1+CD25-) WT

Significance: 2.51903e-18

absent
activated non-Tfh (CD4+CD44+CXCR5-PD1-CD25-) MUT

Significance: 1.02977e-18

absent
Tfr (CD4+CD44+CXCR5+PD1+CD25+) MUT

Significance: 1.54524e-16

absent
naive CD4+ T (CD4+ CD44-CD62L- CD25-) WT

Significance: 4.06371e-18

absent
naive CD4+ T (CD4+ CD44-CD62L- CD25-) MUT

Significance: 4.628219999999999e-18

absent
CD4+CD8+ CD69lo large (DP precursors)

Significance: 3.35955e-17

absent
CD4+CD8-TCRhi CD69hi CD24hi CD25-(B2m def mice)

Significance: 9.60196e-18

absent
CD4+CD8-TCRhi CD69lo CD24lo CD25- (B2m def mice)

Significance: 3.5937600000000005e-17

absent
CD4+CD8-TCRhi CD25+ Foxp3-

Significance: 1.1914300000000001e-17

absent
CD4+CD8-TCRhi CD25-Foxp3+

Significance: 4.7217600000000007e-17

absent
CD4+CD8-TCRhi CD25+ Foxp3+

Significance: 6.008630000000001e-17

absent
BMDCs(dendritic cell)

Significance: 1.0173e-17

absent
DP

Significance: 5.7324e-16

absent
DN3b

Significance: 9.548049999999999e-18

absent
ES cells (E14)

Significance: 7.83202e-14

absent
Small Intestine

Significance: 2.59842e-18

absent
Large Intestine

Significance: 4.01353e-17

absent
Lung

Significance: 3.57254e-16

absent
Muscle

Significance: 4.22684e-18

absent
Heart

Significance: 1.35814e-16

absent
Adipose

Significance: 2.08843e-18

absent
Mammary tissue

Significance: 5.928260000000001e-17

absent
Adrenal

Significance: 8.95186e-16

absent
testis

Significance: 4.44801e-18

absent
placenta

Significance: 6.22645e-17

absent
spinal cord

Significance: 2.59265e-18

absent
stomach

Significance: 1.23366e-19

absent
pancreas

Significance: 5.6688e-18

absent
Eye- Neural retina

Significance: 7.71542e-18

absent
Eye- Optic nerve

Significance: 2.1405e-19

absent
Brain- Olfactory Bulb

Significance: 1.92493e-18

absent
Brain- Frontal Cortex

Significance: 2.87174e-16

absent
Brain- Putamen

Significance: 5.89893e-17

absent
Brain- Medulla Oblongata

Significance: 9.35442e-18

absent
Brain- Sensorimotor Cortex

Significance: 8.303130000000001e-18

absent
Brain- Cerebellum

Significance: 2.9116799999999996e-17

absent
restingB

Significance: 8.168699999999999e-19

absent
aBCD180

Significance: 7.07052e-20

absent
Long Term HSC

Significance: 6.156990000000001e-18

absent
Short Term HSC

Significance: 8.573e-16

absent
gamma delta TCR wt

Significance: 1.16184e-18

absent
gamma delta TCR Marco

Significance: 5.95937e-19

absent
gamma delta TCR M/S -/-

Significance: 1.88347e-18

absent
NK (+IL2+IL12)

Significance: 5.97833e-19

absent
ILC2 precursor

Significance: 5.565409999999999e-17

absent
NCR+ILC3

Significance: 7.009519999999999e-18

absent
ILC2 (Nippo infected)

Significance: 3.90606e-18

absent
ILC1

Significance: 2.91554e-18

absent
ILC2

Significance: 1.4240700000000003e-16

absent
Act B cell 24h

Significance: 1.36594e-18

absent
Act B cell 24h with oligomycin

Significance: 1.40909e-18

absent
ch12 with quintuple mt

Significance: 9.4729e-19

absent
ch12 wt

Significance: 1.80835e-18

absent
ch12 med14 mt

Significance: 2.57872e-19

absent
ch12 wt with drug

Significance: 8.08032e-18

absent
CLP

Significance: 6.783499999999999e-19

absent
NK cells (liver), CD19-CD3ε-NKp46+DX5+Trail-

Significance: 4.69148e-18

absent
Neutrophils(wt)

Significance: 1.6217e-20

absent
J1 embryonic stem cells

Significance: 1.01595e-14

absent
E14 ES cells

Significance: 9.37071e-14

absent
mouse embryonic stem cells (F1216)

Significance: 1.03429e-15

absent
ESC(129SV/Jae/C57BL6J)

Significance: 1.6788299999999998e-16

absent
Embryonic Stem Cells(v6.5)

Significance: 1.87405e-15

absent
Mammary Gland(WT,Basal Mammary Epithelial Cells)

Significance: 1.52575e-13

absent
WT retina

Significance: 3.55948e-17

absent
cerebellar granule cell precursors(wt)

Significance: 5.13371e-14

absent
ILC2+IL33+IL25

Significance: 3.01295e-17

absent
ILC1(WT)

Significance: 3.5029200000000003e-19

absent
ILC2(WT)

Significance: 1.54571e-17

absent
ILC1_AbxGermFree

Significance: 1.1075299999999999e-18

absent
ILC2_AbxGermFree

Significance: 5.46102e-18

absent
ILC3_AbxGermFree

Significance: 2.02168e-18

absent
CD8 Tcells(day8 post infection LCMV-Armstrong)

Significance: 1.01907e-18

absent
CD8 Tcells (day33 post infection LCMV-Armstrong)

Significance: 2.7091200000000003e-18

absent
CD8 Tcells(day35 post infection LCMV)

Significance: 1.34264e-16

absent
Spleen CD8+ T cell (Effector)

Significance: 2.17375e-18

absent
D5 effector TCR SV40-I CD8 T cells

Significance: 6.566279999999999e-19

absent
central memory TCR SV40-I CD8 T cells

Significance: 2.11678e-18

absent
TCR SV40-I CD8 T cells isolated D7 from early malignant lesions

Significance: 4.9653799999999995e-18

absent
TCR SV40-I CD8 T cells isolated D21 from early malignant lesions

Significance: 1.2730999999999998e-17

absent
TCR SV40-I CD8 T cells isolated D28 from early malignant lesions

Significance: 2.9685800000000003e-18

absent
TCR SV40-I CD8 T cells isolated D35 from early malignant lesions

Significance: 2.58525e-17

absent
TCR SV40-I CD8 T cells isolated D60 from early malignant lesions

Significance: 4.51683e-17

absent
memory TCR SV40-I CD8 T cells isolated D35 from established tumors (with listeria immunization)

Significance: 1.08799e-16

absent
memory TCR SV40-I CD8 T cells isolated D14 from established tumors (without listeria immunization)

Significance: 7.24583e-17

absent
Invariant NKT (iNKT) cells

Significance: 8.796059999999999e-19

absent
Splenic B cell

Significance: 2.82521e-20

absent
Bone marrow derived pre-B cell

Significance: 1.6483599999999997e-18

absent
B220+CD43+ B cells

Significance: 2.91461e-17

absent
bone marrow-derived macrophages (Unstimulated)

Significance: 2.9082299999999997e-18

absent
Ckit Mice cells AE9a (AML)

Significance: 2.7681100000000003e-17

absent
dendritic cell(100 ng/mL Lipopolysaccharide, 6hours)

Significance: 9.73687e-18

absent
dendritic cell(100 ng/mL Lipopolysaccharide, 2hours)

Significance: 6.695269999999999e-18

absent
Primary bone marrow derived dendritic cells (DCs, control vector)

Significance: 6.5967300000000005e-18

absent
rod photoreceptors

Significance: 8.75378e-18

absent
WT rod photoreceptors,retina

Significance: 3.66008e-19

absent
green cone photoreceptors

Significance: 7.79616e-19

absent
blue cone photoreceptors/NrlKO

Significance: 2.1806799999999996e-18

absent
WT cone photoreceptors

Significance: 3.49371e-17

absent
embryo_3rd rhombomere (E8.5, wt)

Significance: 9.68241e-15

absent
embryo_3rd rhombomere (E8.5, deltaC)

Significance: 1.20975e-15

absent
embryo_5th rhombomere(E8.5, deltaC)

Significance: 1.0960699999999999e-15

absent
embryo_5th rhombomere(e9.5, wt)

Significance: 3.54823e-15

absent
embryo_5th rhombomere(E8.5, WT)

Significance: 2.49599e-13

absent
embryo_5th rhombomere (E8.5. deltaA)

Significance: 2.43854e-13

absent
embryo_posterior part (E9.5, WT)

Significance: 1.0472299999999999e-16

absent
embryo_posterior part (E8.5, wt)

Significance: 1.5974700000000003e-14

absent
embryo_posterior part(E8.5, deltaA)

Significance: 5.50611e-14

absent
embryo_posterior part (E8.5, deltaC)

Significance: 1.7054200000000002e-13

absent
adult skin epithelia

Significance: 9.62664e-15

absent
Mouse back skin

Significance: 2.3754499999999997e-13

absent
Cranial neural crest cells (E10.5,WT)

Significance: 2.85733e-15

absent
neural progenitor cells(F129)

Significance: 2.99755e-16

absent
neural progenitor cells(Ch13)

Significance: 2.48403e-15

absent
neural progenitor cells(mE6)

Significance: 4.24868e-15

absent
parvalbumin-positive (PV) inhibitory neurons

Significance: 1.01221e-13

absent
vasoactive intestinal peptide-positive (VIP) inhibitory neurons

Significance: 1.4880800000000001e-15

absent
Granule Neuron Progenitors (wt)

Significance: 6.35632e-15

absent
E16.5 sorted germ cells(wt)

Significance: 1.19403e-16

absent
Thymus MECs (Aire+/+)

Significance: 7.73771e-17

absent
FACS-purified corticotrope cells

Significance: 9.12177e-18

absent
FACS-purified melanotrope cells

Significance: 2.48676e-15

absent
ZHBTC4 ES untreated

Significance: 3.1786999999999998e-15

absent
ZHBTC4 ES doxycycline-treated

Significance: 2.8478800000000004e-14

absent
ZHBTC4 ES Brg1fl/fl untreated

Significance: 6.73963e-13

absent
JM8.N4 Asynchronous

Significance: 2.3079799999999997e-19

absent
JM8.N4 Mitosis

Significance: 5.317289999999999e-19

absent
Megakaryocyte primary cell

Significance: 1.73001e-17

absent
Erythroid progenitor primary cell

Significance: 2.5871599999999996e-19

absent
Megakaryocyte-erythroid progenitor cell

Significance: 7.33318e-19

absent
Erythroblast primary cell

Significance: 2.78804e-19

absent
Megakaryocyte progenitor cell

Significance: 1.3406600000000002e-17

absent
Common myeloid progenitor primary cell

Significance: 6.63388e-18

absent
dendritic cell(100 ng/mL Lipopolysaccharide, 4hours)

Significance: 2.5955900000000005e-17

absent
Granulocyte monocyte progenitor primary cell

Significance: 1.3264000000000001e-17

absent
dendritic in vitro differentiated cells

Significance: 8.900080000000001e-17

absent
Undifferentiated mouse embryonic stem cells (ZhBTc4)

Significance: 2.51838e-15

absent
Embryonic day 0 (stem cell, ES-CJ7)

Significance: 6.732940000000001e-15

Significance: 7.39133e-08

absent
fibroblast/NIH-3T3

Significance: 1.70195e-16

absent
Liver (Adult 8 weeks)

Significance: 1.0958e-15

absent
Lung (adult-8wks)

Significance: 2.96953e-16

absent
murine mammary adenocarcinoma cell line(3134 cell line)

Significance: 2.64153e-17

absent
Blast-cultured splenic CD4+ T-cells

Significance: 2.9468e-18

absent
Naive splenic CD4+ T-cells

Significance: 1.76863e-18

absent
Regulatory T cells CD4+,CD25+

Significance: 2.33735e-15

absent
Activated primary CD4 effector cells, isolated ex vivo

Significance: 3.43135e-18

absent
mouse spleen B cells, CD43-,CD11b- (immature B cells)

Significance: 1.19358e-15

absent
myeloid progenitor cells, CD34+ (416B)

Significance: 1.7519999999999997e-16

absent
Whole Brain (adult-8wks)

Significance: 2.9716000000000006e-14

absent
Whole Brain (E14.5)

Significance: 4.78212e-15

absent
Mus musculus strain 129S1/SVImJ ES-CJ7 stem cell male embryo

Significance: 3.3695499999999997e-16

absent
mouse embryonic stem cells E14

Significance: 5.69952e-16

absent
Mus musculus strain C57BL/6J R1 stem cell

Significance: 1.12436e-15

absent
mouse embryo fibroblasts/3T3-L1

Significance: 3.1928899999999997e-17

absent
kidney (P0)

Significance: 4.4577e-15

absent
Kidney(adult-8wks)

Significance: 3.9081099999999995e-16

absent
Liver(adult-8wks)

Significance: 2.31678e-15

absent
Liver(E14.5)

Significance: 2.0071900000000003e-18

absent
liver(P0)

Significance: 1.42639e-18

absent
Lung(adult-8wks)

Significance: 1.12885e-15

absent
lung(P0)

Significance: 2.39298e-15

absent
Mouse lung (E14.5)

Significance: 1.4307e-16

absent
Mus musculus C57BL/6 adipocyte was differentiated from 3T3-L1 (Day 8)

Significance: 2.27042e-17

absent
Adipose tissue

Significance: 1.6087099999999999e-15

absent
Cerebellum

Significance: 3.29143e-18

absent
CD4-positive helper(adult-8wks, Activated primary CD4 effector cells)

Significance: 8.1892e-15

absent
CD4-positive, CD25-positive, alpha-beta regulatory T cell(adult-8wks)

Significance: 2.5744200000000002e-18

absent
c-Kit-positive CD71-positive TER-119-positive erythroid progenitor cells

Significance: 2.1082600000000002e-17

absent
Mesoderm(E11.5)

Significance: 3.04287e-12

absent
mixed embryonic mouse forebrain(E14.5)

Significance: 1.01754e-13

absent
forebrain(P0)

Significance: 8.1026e-15

absent
mixed mouse hindbrain(P0)

Significance: 3.1683000000000002e-15

absent
hindbrain embryo(E14.5)

Significance: 5.62719e-15

absent
mixed embryonic mouse midbrain(E14.5)

Significance: 9.377290000000001e-13

absent
midbrain embryo(E11.5)

Significance: 1.68582e-15

Significance: 0.00045687

absent
midbrain(P0)

Significance: 1.23241e-14

absent
Whole Brain(E14.5)

Significance: 8.339960000000001e-14

absent
Whole Brain(adult-8wks)

Significance: 4.83847e-14

absent
telencephalon tissue

Significance: 1.23779e-15

absent
mixed embryonic mouse limb(E14.5)

Significance: 1.8162599999999999e-16

absent
mixed embryonic mouse limb(E11.5)

Significance: 6.02893e-15

absent
embryo forelimb buds(E11.5)

Significance: 7.223960000000001e-16

absent
embryo hindlimb buds (E11.5)

Significance: 2.18689e-16

absent
embryonic facial prominence(e14.5)

Significance: 4.78484e-13

absent
embryonic facial prominence(e11.5)

Significance: 9.154840000000001e-16

absent
neural tube embryo(E11.5)

Significance: 2.83708e-16

absent
Large Intestine (adult-8wks)

Significance: 3.72359e-17

absent
stomach(P0)

Significance: 1.82987e-15

absent
spleen(adult-8wks)

Significance: 6.92424e-19

absent
Mouse hematopoietic suspension cell line positive for CD34(416B cell line)

Significance: 7.28724e-15

absent
Murine B-lymphoma cell line(A20 cell line)

Significance: 1.0171299999999998e-16

absent
acute myeloid leukemia

Significance: 2.4002600000000002e-17

absent
MEL-GATA-1-ER cell line

Significance: 1.16675e-16

absent
MEL cell line

Significance: 2.3151599999999997e-18

absent
MEL cell line treated with 125 uM zinc dichloride for 24 hours

Significance: 6.38204e-17

absent
NIH3T3

Significance: 3.6299e-16

absent
cholinergic motor neuron cell line MN1 treated with 10 nM methyltrienolone

Significance: 2.4514000000000003e-16

absent
MN1 cell line

Significance: 6.151359999999999e-16

absent
3T3-L1

Significance: 1.10242e-17

absent
Unique Cell types only Homer finds Smarcc2
Cell typeModiscoHomer
excitatory pyramidal neuronsabsent

Significance: 7.34344e-07