In [1]:
# Parameters
data_name = "Creb3"
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.
2019-07-25 23:23:44,249 [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 Creb3: M5323_1.02
Shared Cell types both TF-MoDISco and Homer finds Creb3
Cell typeModiscoHomer
stomach(P0)

Significance: 6.389940000000001e-06

Significance: 0.0023324

murine mammary adenocarcinoma cell line(3134 cell line)

Significance: 2.4222100000000004e-07

Significance: 0.00282393

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

Significance: 1.03984e-06

Significance: 0.0066184

bone marrow-derived macrophages (Unstimulated)

Significance: 5.88982e-07

Significance: 0.00758007

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

Significance: 2.17908e-06

Significance: 4.376270000000001e-05

Ter119+ Erythroid cells

Significance: 0.000236729

Significance: 0.0109664

CH12.LX cell line

Significance: 3.62388e-07

Significance: 0.000163189

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

Significance: 1.17077e-05

Significance: 1.19874e-05

MN1 cell line

Significance: 5.35072e-08

Significance: 4.4873e-05

neutrophils

Significance: 1.68697e-05

Significance: 0.00712058

green cone photoreceptors

Significance: 0.00010428700000000001

Significance: 0.00188495

embryo_5th rhombomere(e9.5, wt)

Significance: 3.56099e-05

Significance: 0.00020790099999999997

CD4+CD8int TCRhi CD69hi CD24hi (B2m def mice)

Significance: 0.000240164

Significance: 0.00302238

neural progenitor cells(G4)

Significance: 4.37851e-05

Significance: 0.0011792

neural progenitor cells(Ch13)

Significance: 4.0179699999999995e-09

Significance: 4.719940000000001e-06

MEFs

Significance: 1.9546e-06

Significance: 4.92737e-05

Adipose

Significance: 0.000181455

Significance: 0.00436267

Megakaryocyte progenitor cell

Significance: 0.00046024300000000005

Significance: 0.00924796

fibroblast/NIH-3T3

Significance: 6.773810000000001e-07

Significance: 0.00106119

ch12 wt with drug

Significance: 2.84496e-05

Significance: 0.00249184

mouse embryo fibroblasts/3T3-L1

Significance: 5.683429999999999e-07

Significance: 0.00190688

Embryonic Stem Cells(v6.5)

Significance: 3.14899e-06

Significance: 0.00528271

myeloid progenitor cells, CD34+ (416B)

Significance: 0.000348732

Significance: 0.00787504

midbrain(P0)

Significance: 7.561650000000001e-08

Significance: 0.00149872

Unique Cell types only TF-MoDISco finds Creb3
Cell typeModiscoHomer
immature B cells

Significance: 0.00471797

absent
mature B cells

Significance: 5.55795e-05

absent
GC B cells

Significance: 0.000173687

absent
plasma cells

Significance: 1.37764e-05

absent
aB LPS

Significance: 5.64873e-05

absent
aB LPS+a-d-dextran

Significance: 3.16449e-05

absent
Tfh from infected with LCMV

Significance: 0.00130458

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

Significance: 3.98207e-06

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

Significance: 4.3635600000000006e-05

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

Significance: 0.000230429

absent
CD4+CD8+ CD69lo large (DP precursors)

Significance: 0.000536758

absent
CD4+CD8+ CD69lo small (DP precursors)

Significance: 0.000237565

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

Significance: 0.000101598

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

Significance: 0.000188018

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

Significance: 0.00134399

absent
CD4+CD8-TCRhi CD25+ Foxp3-

Significance: 0.000440615

absent
DP

Significance: 0.0007326189999999999

absent
DN3a

Significance: 6.46875e-05

absent
DN3b

Significance: 6.56456e-05

absent
Small Intestine

Significance: 0.00117154

absent
Lung

Significance: 1.6511400000000003e-05

absent
Heart

Significance: 1.8961700000000002e-05

absent
Adrenal

Significance: 7.75739e-05

absent
testis

Significance: 0.025034900000000002

absent
spinal cord

Significance: 0.000174649

absent
stomach

Significance: 0.000246777

absent
Eye- Neural retina

Significance: 0.000305106

absent
Eye- Optic nerve

Significance: 2.29893e-06

absent
Brain- Frontal Cortex

Significance: 0.00245381

absent
Brain- Medulla Oblongata

Significance: 1.8503299999999999e-06

absent
aBCD180

Significance: 0.00019837700000000002

absent
ILC1

Significance: 5.2861599999999995e-05

absent
NCR+ILC3+IL23

Significance: 6.774920000000001e-07

absent
Act B cell 24h

Significance: 0.0006362809999999999

absent
ch12 with quintuple mt

Significance: 0.00437477

absent
ch12 med14 mt

Significance: 0.0008868319999999999

absent
CLP

Significance: 0.000294886

absent
Spleen CD8+ T cell(MPEC)

Significance: 0.000285592

absent
J1 embryonic stem cells

Significance: 1.36247e-05

absent
E14 ES cells

Significance: 0.000382791

absent
mouse embryonic stem cells (F1216)

Significance: 0.00125663

absent
ESC(129SV/Jae/C57BL6J)

Significance: 0.00032943199999999995

absent
cerebellar granule cell precursors(wt)

Significance: 8.47741e-07

absent
ILC3(WT)

Significance: 9.65648e-06

absent
Naive CD8+ T cell

Significance: 0.000327042

absent
CD8 Tcells(day8 post infection LCMV-Armstrong)

Significance: 6.40256e-05

absent
CD8 Tcells (day33 post infection LCMV-Armstrong)

Significance: 1.9949100000000002e-05

absent
Spleen CD8+ T cell(SLEC)

Significance: 0.000131998

absent
naive transgenic TCR SV40-I CD8 T cells

Significance: 0.000157799

absent
D7 effector TCR SV40-I CD8 T cells

Significance: 3.11028e-05

absent
central memory TCR SV40-I CD8 T cells

Significance: 0.000102355

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

Significance: 0.00021602900000000001

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

Significance: 1.37835e-05

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

Significance: 2.9454299999999997e-05

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

Significance: 0.000118155

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

Significance: 1.77324e-05

absent
Invariant NKT (iNKT) cells

Significance: 6.964119999999999e-05

absent
Act B cell

Significance: 0.00011837

absent
Pre-PB

Significance: 0.00191603

absent
Bone marrow derived pre-B cell

Significance: 6.09128e-05

absent
B220+CD43+ B cells

Significance: 0.00232793

absent
Ckit Mice cells AE9a (AML)

Significance: 1.59531e-07

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

Significance: 2.2139700000000003e-06

absent
ES_derived Definitive Endoderm

Significance: 0.000393001

absent
rod photoreceptors

Significance: 8.28808e-05

absent
WT rod photoreceptors,retina

Significance: 0.000120264

absent
blue cone photoreceptors/NrlKO

Significance: 8.59035e-05

absent
embryo_3rd rhombomere (E8.5, deltaA)

Significance: 0.000592496

absent
embryo_3rd rhombomere (E8.5, wt)

Significance: 6.92172e-05

absent
embryo_3rd rhombomere (E8.5, deltaC)

Significance: 0.000153195

absent
embryo_5th rhombomere(E8.5, deltaC)

Significance: 0.000237099

absent
embryo_posterior part (E9.5, WT)

Significance: 0.000167025

absent
embryo_posterior part (E8.5, wt)

Significance: 0.00024124200000000002

absent
embryo_posterior part(E8.5, deltaA)

Significance: 6.90687e-05

absent
embryo_posterior part (E8.5, deltaC)

Significance: 0.000540298

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

Significance: 1.66834e-05

absent
neural progenitor cells(F129)

Significance: 1.7992500000000002e-06

absent
neural progenitor cells(mE6)

Significance: 3.7413800000000004e-05

absent
excitatory pyramidal neurons

Significance: 0.00098174

absent
vasoactive intestinal peptide-positive (VIP) inhibitory neurons

Significance: 2.15452e-06

absent
Granule Neuron Progenitors (wt)

Significance: 2.5267099999999997e-07

absent
FACS-purified corticotrope cells

Significance: 2.8165500000000003e-05

absent
ZHBTC4 ES Brg1fl/fl untreated

Significance: 7.16828e-07

absent
JM8.N4 Asynchronous

Significance: 0.000170713

absent
JM8.N4 Mitosis

Significance: 0.000163629

absent
Megakaryocyte primary cell

Significance: 2.96461e-05

absent
Erythroid progenitor primary cell

Significance: 0.000105508

absent
Megakaryocyte-erythroid progenitor cell

Significance: 0.000172085

absent
Erythroblast primary cell

Significance: 6.64047e-05

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

Significance: 1.75563e-06

absent
dendritic in vitro differentiated cells

Significance: 4.1028800000000004e-06

absent
Undifferentiated mouse embryonic stem cells (ZhBTc4)

Significance: 0.000110411

absent
murine mammary adenocarcinoma cell line(3134 cell line)

Significance: 9.873389999999998e-08

absent
Blast-cultured splenic CD4+ T-cells

Significance: 3.94669e-05

absent
Activated primary CD4 effector cells, isolated ex vivo

Significance: 0.000110844

absent
Mus musculus strain C57BL/6J R1 stem cell

Significance: 0.000438529

absent
Fibroblast/NIH3T3

Significance: 2.5553e-07

absent
Fibroblast (adult-8wks)

Significance: 6.707210000000001e-08

absent
Liver(E14.5)

Significance: 0.00015653

absent
Mouse lung (E14.5)

Significance: 1.4371099999999999e-05

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

Significance: 0.00112782

absent
mixed embryonic mouse retina(E14.5)

Significance: 0.000319924

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

Significance: 7.95863e-05

absent
Mesoderm(E11.5)

Significance: 9.28154e-06

absent
forebrain(P0)

Significance: 1.07376e-05

absent
mixed embryonic mouse hindbrain(E11.5)

Significance: 1.0134700000000001e-06

absent
hindbrain embryo(E14.5)

Significance: 8.849769999999999e-06

absent
mixed embryonic mouse midbrain(E14.5)

Significance: 4.64939e-06

absent
midbrain embryo(E11.5)

Significance: 3.0227800000000004e-06

absent
Whole Brain(E14.5)

Significance: 3.9376e-06

absent
telencephalon tissue

Significance: 6.277869999999999e-06

absent
mixed embryonic mouse limb(E14.5)

Significance: 2.67709e-06

absent
mixed embryonic mouse limb(E11.5)

Significance: 0.000198292

absent
embryo forelimb buds(E11.5)

Significance: 0.000754162

absent
embryo hindlimb buds (E11.5)

Significance: 4.3457799999999996e-05

absent
embryonic facial prominence(e11.5)

Significance: 2.0607400000000003e-06

absent
neural tube embryo(E11.5)

Significance: 6.57088e-07

absent
Large Intestine (adult-8wks)

Significance: 7.39983e-07

absent
acute myeloid leukemia

Significance: 6.18495e-07

absent
MEL-GATA-1-ER cell line

Significance: 2.0684299999999998e-05

absent
MEL cell line

Significance: 4.425399999999999e-05

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

Significance: 2.6694499999999997e-05

absent
NIH3T3

Significance: 4.5160400000000005e-07

absent
3T3-L1

Significance: 2.6149400000000003e-08

absent
Unique Cell types only Homer finds Creb3
Cell typeModiscoHomer
MPPabsent

Significance: 0.00376994

naive CD8absent

Significance: 0.00127852

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

Significance: 0.000255405

Common myeloid progenitor primary cellabsent

Significance: 0.00198572

embryonic facial prominence(e14.5)absent

Significance: 0.00387395

lung(P0)absent

Significance: 0.00038789999999999994

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

Significance: 0.00347319

Mammary Gland(WT,Basal Mammary Epithelial Cells)absent

Significance: 6.89944e-05

heart tissue(P0)absent

Significance: 0.013875100000000001

spleen(adult-8wks)absent

Significance: 0.0143688

ILC1(WT)absent

Significance: 0.00184875

gamma delta TCR Marcoabsent

Significance: 0.0260546

cholinergic motor neuron cell line MN1 treated with 10 nM methyltrienoloneabsent

Significance: 1.23916e-05

CD8 Tcells(day35 post infection LCMV)absent

Significance: 0.00148646

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

Significance: 0.00373016