In [1]:
# Parameters
data_name = "Mbtps2"
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 00:50:54,435 [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 Mbtps2: M1919_1.02

Shared Cell types both TF-MoDISco and Homer finds Mbtps2
Cell typeModiscoHomer
TCR SV40-I CD8 T cells isolated D28 from early malignant lesions

Significance: 5.9145100000000004e-05

Significance: 0.00023073400000000002

naive CD8

Significance: 2.76122e-05

Significance: 0.00735157

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

Significance: 2.73293e-05

Significance: 0.00232434

mixed embryonic mouse limb(E11.5)

Significance: 0.00030087

Significance: 0.00790723

proB cells

Significance: 3.24242e-05

Significance: 0.000502912

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

Significance: 1.60309e-05

Significance: 0.00489839

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

Significance: 2.5299e-05

Significance: 0.039382099999999996

mature B cells

Significance: 1.80538e-05

Significance: 0.00580761

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

Significance: 1.84228e-05

Significance: 0.0181416

B1 B cells

Significance: 3.93494e-05

Significance: 0.000268157

Pre-PB

Significance: 1.43347e-05

Significance: 0.00045275

plasma cells

Significance: 0.000151896

Significance: 0.000283095

Large Intestine (adult-8wks)

Significance: 5.39475e-06

Significance: 0.000378223

aB LPS+IL4

Significance: 4.2640200000000006e-05

Significance: 0.00150281

aB LPS+IL21

Significance: 7.869149999999999e-05

Significance: 1.7424299999999998e-07

CH12.LX cell line

Significance: 9.36404e-06

Significance: 4.7391399999999995e-06

Ckit Mice cells AE9a (AML)

Significance: 8.861809999999999e-05

Significance: 0.00137494

mast cells

Significance: 1.36517e-05

Significance: 3.63052e-08

basophils

Significance: 1.51101e-05

Significance: 0.030044900000000003

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

Significance: 4.9881000000000006e-05

Significance: 0.00043716

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

Significance: 2.66913e-05

Significance: 0.00192157

NIH3T3

Significance: 8.43029e-06

Significance: 0.00409965

Tfh from infected with LCMV

Significance: 1.5741700000000002e-05

Significance: 0.000262875

3T3-L1

Significance: 6.10697e-06

Significance: 9.59323e-06

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

Significance: 1.21345e-05

Significance: 1.8787599999999999e-06

WT cone photoreceptors

Significance: 0.00042639999999999996

Significance: 0.000541532

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

Significance: 4.23437e-05

Significance: 1.3127100000000002e-06

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

Significance: 2.5155100000000002e-05

Significance: 2.2973199999999998e-07

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

Significance: 4.0551e-05

Significance: 2.17617e-08

CD4+CD8-TCRhi CD25-Foxp3+

Significance: 2.17953e-05

Significance: 0.013810499999999998

CD4+CD8-TCRhi CD25+ Foxp3+

Significance: 1.6629e-05

Significance: 0.00226143

macrophage

Significance: 1.66644e-05

Significance: 0.00033033

skeletal muscle tissue(adult-8wks)

Significance: 9.302460000000002e-06

Significance: 0.0284058

JM8.N4 Asynchronous

Significance: 1.3333800000000001e-05

Significance: 0.0648843

spleen(adult-8wks)

Significance: 1.1603699999999999e-05

Significance: 2.8986e-05

placenta

Significance: 2.87071e-05

Significance: 0.00874616

spinal cord

Significance: 2.0731999999999997e-05

Significance: 4.678859999999999e-09

stomach

Significance: 1.31772e-05

Significance: 7.58652e-05

Erythroid progenitor primary cell

Significance: 1.82758e-05

Significance: 9.53693e-08

Erythroblast primary cell

Significance: 2.1074000000000002e-05

Significance: 0.000160564

murine mammary adenocarcinoma cell line(3134 cell line)

Significance: 1.50847e-05

Significance: 0.00018062099999999998

Brain- Frontal Cortex

Significance: 9.067879999999999e-05

Significance: 0.000242721

fibroblast/NIH-3T3

Significance: 4.5315500000000003e-05

Significance: 0.027580200000000003

aBCD180

Significance: 1.2336199999999999e-05

Significance: 6.532369999999999e-05

acute myeloid leukemia

Significance: 1.74356e-05

Significance: 0.0028363000000000004

NK (+IL2+IL12)

Significance: 2.71286e-05

Significance: 0.0008300089999999999

ILC2 precursor

Significance: 1.53204e-05

Significance: 0.000184677

NCR+ILC3

Significance: 1.5618e-05

Significance: 7.692829999999999e-07

Activated primary CD4 effector cells, isolated ex vivo

Significance: 1.14319e-05

Significance: 0.000143871

myeloid progenitor cells, CD34+ (416B)

Significance: 1.2377899999999999e-05

Significance: 9.64347e-06

Act B cell 24h

Significance: 3.62214e-05

Significance: 0.000697337

Act B cell 24h with oligomycin

Significance: 7.17805e-06

Significance: 0.07444680000000001

ch12 wt

Significance: 1.72617e-05

Significance: 0.000199017

Fibroblast/NIH3T3

Significance: 9.15205e-06

Significance: 0.00223451

mouse embryo fibroblasts/3T3-L1

Significance: 3.35885e-05

Significance: 1.2375199999999998e-07

liver(P0)

Significance: 1.3858099999999999e-05

Significance: 1.92706e-06

lung(P0)

Significance: 5.8696e-05

Significance: 0.00323716

Heart (adult-8wks)

Significance: 0.000106313

Significance: 0.019021400000000004

ILC1(WT)

Significance: 2.3876799999999998e-05

Significance: 0.00216944

ILC2(WT)

Significance: 3.49506e-05

Significance: 0.00041887099999999997

mixed embryonic mouse retina(E14.5)

Significance: 5.5177600000000005e-05

Significance: 0.0009031289999999999

ILC1_AbxGermFree

Significance: 3.11698e-05

Significance: 0.000183893

ILC2_AbxGermFree

Significance: 6.87597e-05

Significance: 7.605180000000001e-05

ILC3_AbxGermFree

Significance: 4.20943e-05

Significance: 0.000409688

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

Significance: 1.39526e-05

Significance: 0.000579622

CD8 Tcells(day8 post infection LCMV-Armstrong)

Significance: 1.2596800000000001e-05

Significance: 0.00038746

CD8 Tcells (day33 post infection LCMV-Armstrong)

Significance: 2.77086e-05

Significance: 1.08993e-06

Spleen CD8+ T cell (Effector)

Significance: 7.38508e-06

Significance: 0.00047966400000000003

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

Significance: 2.01462e-05

Significance: 0.00021888799999999998

Spleen CD8+ T cell(SLEC)

Significance: 1.44049e-05

Significance: 0.000191736

D7 effector TCR SV40-I CD8 T cells

Significance: 2.2124099999999997e-05

Significance: 0.00842362

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

Significance: 8.03874e-05

Significance: 0.000347921

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

Significance: 5.94178e-06

Significance: 0.000147009

telencephalon tissue

Significance: 9.029580000000001e-06

Significance: 0.0164015

Unique Cell types only TF-MoDISco finds Mbtps2
Cell typeModiscoHomer
MPP

Significance: 1.63354e-05

absent
CD25CCR6 DN CD4 (memory CD4+ T cell)

Significance: 1.41637e-05

absent
Th17 CD4

Significance: 3.10404e-05

absent
NK cells (spleen)

Significance: 1.60193e-05

absent
preB cells

Significance: 1.8218299999999998e-05

absent
immature B cells

Significance: 3.17903e-05

absent
GC B cells

Significance: 1.87838e-05

absent
aB LPS

Significance: 2.73199e-05

absent
aB LPS+a-d-dextran

Significance: 2.62867e-05

absent
aB aCD40+IL4

Significance: 1.21739e-05

absent
eosinphils (ex-vivo, BalbC)

Significance: 0.00011779

absent
eosinophils (isolated from spleens, BalbC)

Significance: 2.0809299999999997e-05

absent
neutrophils

Significance: 2.92471e-05

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

Significance: 8.70343e-06

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

Significance: 2.1618400000000003e-05

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

Significance: 1.51467e-05

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

Significance: 4.57207e-05

absent
CD4+CD8+ CD69lo large (DP precursors)

Significance: 1.31986e-05

absent
CD4+CD8+ CD69lo small (DP precursors)

Significance: 1.29575e-05

absent
CD4+CD8int TCRhi CD69hi CD24hi (B2m def mice)

Significance: 1.5042699999999999e-05

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

Significance: 2.0181e-05

absent
CD4+CD8int TCRhi CD69hi CD24hi (MHCII def mice)

Significance: 3.3047600000000005e-05

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

Significance: 9.591600000000001e-05

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

Significance: 2.39769e-05

absent
CD4+CD8-TCRhi CD25+ Foxp3-

Significance: 3.40172e-05

absent
BMDCs(dendritic cell)

Significance: 2.0635100000000002e-05

absent
Erythroblasts

Significance: 1.34984e-05

absent
DP

Significance: 1.73659e-05

absent
DN3a

Significance: 5.63174e-05

absent
ISP (Immature single positive)

Significance: 1.31064e-05

absent
MEFs

Significance: 4.29142e-05

absent
Small Intestine

Significance: 0.000179448

absent
Large Intestine

Significance: 6.27891e-05

absent
Lung

Significance: 2.63227e-05

absent
Muscle

Significance: 5.2284099999999996e-05

absent
Heart

Significance: 8.268290000000001e-05

absent
Adipose

Significance: 2.46581e-05

absent
Adrenal

Significance: 8.06198e-05

absent
testis

Significance: 2.58521e-05

absent
pancreas

Significance: 6.623189999999999e-05

absent
Eye- Neural retina

Significance: 6.41257e-05

absent
Eye- Optic nerve

Significance: 3.5516300000000004e-05

absent
Brain- Olfactory Bulb

Significance: 3.16744e-05

absent
Brain- Putamen

Significance: 3.09949e-05

absent
Brain- Medulla Oblongata

Significance: 2.65864e-05

absent
Brain- Sensorimotor Cortex

Significance: 4.979980000000001e-06

absent
Brain- Cerebellum

Significance: 3.77683e-05

absent
restingB

Significance: 1.2322e-05

absent
Long Term HSC

Significance: 2.9679899999999997e-05

absent
Short Term HSC

Significance: 3.74498e-05

absent
gamma delta TCR wt

Significance: 2.26544e-05

absent
gamma delta TCR Marco

Significance: 1.43508e-05

absent
gamma delta TCR M/S -/-

Significance: 1.84016e-05

absent
ILC2 (Nippo infected)

Significance: 5.1650900000000004e-05

absent
ILC1

Significance: 4.05512e-05

absent
NCR+ILC3+IL23

Significance: 1.68045e-05

absent
ILC2

Significance: 2.27335e-05

absent
ch12 with quintuple mt

Significance: 7.961130000000001e-06

absent
ch12 med14 mt

Significance: 1.04488e-05

absent
ch12 wt with drug

Significance: 7.57564e-05

absent
CLP

Significance: 2.1457600000000003e-05

absent
Spleen CD8+ T cell(MPEC)

Significance: 1.4906900000000001e-05

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

Significance: 0.000123159

absent
Neutrophils(wt)

Significance: 2.02056e-05

absent
E14 ES cells

Significance: 2.03354e-05

absent
mouse embryonic stem cells (F1216)

Significance: 5.53819e-05

absent
ESC(129SV/Jae/C57BL6J)

Significance: 2.9383499999999997e-05

absent
Embryonic Stem Cells(v6.5)

Significance: 8.24117e-05

absent
Mammary Gland(WT,Basal Mammary Epithelial Cells)

Significance: 0.00041671300000000003

absent
WT retina

Significance: 1.8833e-05

absent
ILC2+IL33+IL25

Significance: 1.38293e-05

absent
ILC3(WT)

Significance: 9.85091e-05

absent
Naive CD8+ T cell

Significance: 2.28712e-05

absent
CD8 Tcells(day35 post infection LCMV)

Significance: 3.69276e-05

absent
Spleen CD8+ T cell (Exhausted)

Significance: 1.4626300000000001e-05

absent
naive transgenic TCR SV40-I CD8 T cells

Significance: 8.31339e-06

absent
central memory TCR SV40-I CD8 T cells

Significance: 8.97191e-06

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

Significance: 1.6655999999999998e-05

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

Significance: 1.66346e-05

absent
memory TCR SV40-I CD8 T cells isolated D7 from established tumors (with listeria immunization)

Significance: 3.0128800000000002e-05

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

Significance: 2.4263400000000002e-05

absent
Invariant NKT (iNKT) cells

Significance: 1.21451e-05

absent
Act B cell

Significance: 1.1359000000000001e-05

absent
Splenic B cell

Significance: 1.25236e-05

absent
Bone marrow derived pre-B cell

Significance: 3.32782e-05

absent
B220+CD43+ B cells

Significance: 1.09176e-05

absent
bone marrow-derived macrophages (Unstimulated)

Significance: 1.3229500000000001e-05

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

Significance: 7.4319299999999995e-06

absent
Ter119+ Erythroid cells

Significance: 3.23567e-05

absent
ES_derived Definitive Endoderm

Significance: 9.05758e-06

absent
rod photoreceptors

Significance: 9.54817e-06

absent
WT rod photoreceptors,retina

Significance: 6.4694e-06

absent
green cone photoreceptors

Significance: 1.85477e-05

absent
blue cone photoreceptors/NrlKO

Significance: 1.4651800000000001e-05

absent
embryo_3rd rhombomere (E8.5, deltaA)

Significance: 7.97469e-05

absent
embryo_3rd rhombomere (E8.5, deltaC)

Significance: 0.000136909

absent
embryo_5th rhombomere(E8.5, deltaC)

Significance: 6.44174e-05

absent
embryo_5th rhombomere(E8.5, WT)

Significance: 0.000143785

absent
embryo_posterior part(E8.5, deltaA)

Significance: 0.00033539800000000004

absent
embryo_posterior part (E8.5, deltaC)

Significance: 0.00017318299999999998

absent
adult skin epithelia

Significance: 0.000104496

absent
Mouse back skin

Significance: 0.000116416

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

Significance: 0.00020040099999999998

absent
neural progenitor cells(F129)

Significance: 2.96271e-05

absent
neural progenitor cells(G4)

Significance: 3.25017e-05

absent
excitatory pyramidal neurons

Significance: 8.10998e-06

absent
parvalbumin-positive (PV) inhibitory neurons

Significance: 4.55173e-05

absent
vasoactive intestinal peptide-positive (VIP) inhibitory neurons

Significance: 4.92346e-05

absent
Cortical excitatory neurons

Significance: 7.479410000000001e-06

absent
Granule Neuron Progenitors (wt)

Significance: 4.75646e-05

absent
E16.5 sorted germ cells(wt)

Significance: 6.154069999999999e-06

absent
FACS-purified melanotrope cells

Significance: 8.0354e-05

absent
ZHBTC4 ES doxycycline-treated

Significance: 7.79526e-06

absent
JM8.N4 Mitosis

Significance: 2.53458e-05

absent
Megakaryocyte primary cell

Significance: 1.85337e-05

absent
Megakaryocyte-erythroid progenitor cell

Significance: 1.8494e-05

absent
Megakaryocyte progenitor cell

Significance: 1.69509e-05

absent
Common myeloid progenitor primary cell

Significance: 8.86631e-06

absent
Granulocyte monocyte progenitor primary cell

Significance: 6.31086e-06

absent
dendritic in vitro differentiated cells

Significance: 0.000173316

absent
Undifferentiated mouse embryonic stem cells (ZhBTc4)

Significance: 1.10061e-05

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

Significance: 3.37606e-06

absent
Liver (Adult 8 weeks)

Significance: 1.30002e-05

absent
Lung (adult-8wks)

Significance: 1.80426e-05

absent
murine mammary adenocarcinoma cell line(3134 cell line)

Significance: 3.49388e-05

absent
Blast-cultured splenic CD4+ T-cells

Significance: 9.738910000000002e-06

absent
Naive splenic CD4+ T-cells

Significance: 1.58655e-05

absent
Whole Brain (adult-8wks)

Significance: 2.23559e-05

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

Significance: 1.34551e-05

absent
mouse embryonic stem cells E14

Significance: 8.72344e-06

Significance: 0.0637871

absent
Mus musculus strain C57BL/6J R1 stem cell

Significance: 8.065160000000001e-06

absent
Fibroblast (adult-8wks)

Significance: 1.23775e-05

absent
kidney (P0)

Significance: 0.00010947100000000001

absent
Kidney(adult-8wks)

Significance: 3.34771e-05

absent
Liver(adult-8wks)

Significance: 0.000124321

absent
Liver(E14.5)

Significance: 1.7275799999999998e-05

absent
Lung(adult-8wks)

Significance: 0.00010051

absent
Mouse lung (E14.5)

Significance: 3.58727e-05

absent
heart tissue(P0)

Significance: 2.69506e-05

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

Significance: 0.000126567

absent
Adipose tissue

Significance: 1.24126e-05

absent
Retina(newborn 1 day)

Significance: 2.94166e-05

absent
Cerebellum

Significance: 1.11924e-05

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

Significance: 1.8566300000000002e-05

absent
Mesoderm(E11.5)

Significance: 0.00010785100000000001

absent
Muller cell(P12)

Significance: 0.00010863600000000001

absent
forebrain(P0)

Significance: 6.60522e-05

absent
mixed mouse hindbrain(P0)

Significance: 5.89666e-05

absent
mixed embryonic mouse hindbrain(E11.5)

Significance: 7.522199999999999e-05

absent
hindbrain embryo(E14.5)

Significance: 0.00012987

absent
mixed embryonic mouse midbrain(E14.5)

Significance: 0.00011837

absent
midbrain embryo(E11.5)

Significance: 7.414949999999999e-05

absent
midbrain(P0)

Significance: 5.2685299999999995e-05

absent
Whole Brain(E14.5)

Significance: 1.86694e-05

absent
Whole Brain(adult-8wks)

Significance: 1.57653e-05

absent
mixed embryonic mouse limb(E14.5)

Significance: 3.60043e-05

absent
embryo forelimb buds(E11.5)

Significance: 0.000114974

absent
embryo hindlimb buds (E11.5)

Significance: 5.03489e-06

absent
embryonic facial prominence(e14.5)

Significance: 5.2855699999999996e-05

absent
embryonic facial prominence(e11.5)

Significance: 2.1085999999999998e-05

absent
neural tube embryo(E11.5)

Significance: 8.337379999999999e-05

absent
stomach(P0)

Significance: 8.387089999999999e-06

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

Significance: 1.68945e-05

absent
MEL-GATA-1-ER cell line

Significance: 2.83438e-05

absent
MEL cell line

Significance: 1.27617e-05

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

Significance: 0.000138676

absent
MN1 cell line

Significance: 3.25099e-05

absent
Unique Cell types only Homer finds Mbtps2
Cell typeModiscoHomer
embryo_posterior part (E9.5, WT)absent

Significance: 0.000429956

embryo_posterior part (E8.5, wt)absent

Significance: 0.00527631

MZ B cellsabsent

Significance: 0.0119714

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

Significance: 0.000291194

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

Significance: 6.58543e-05

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

Significance: 2.5857799999999997e-06

D5 effector TCR SV40-I CD8 T cellsabsent

Significance: 0.0008263680000000001

Mammary tissueabsent

Significance: 0.000199084