ISMARA results: Neurod1

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GSE53960: rat RNA-Seq transcriptomic Bodymap

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Results for Neurod1

Z-value: 1.29

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Transcription factors associated with Neurod1

Gene Symbol	Gene ID	Gene Info
Neurod1 NCBI RGD Ensembl	ENSRNOG00000005609	neuronal differentiation 1

Activity-expression correlation:

Gene	Promoter	Pearson corr. coef.	P-value	Plot
Neurod1	rn6_v1_chr3_-_66417741_66417741	0.26	1.6e-06	Click!

Activity profile of Neurod1 motif

Sorted Z-values of Neurod1 motif

Top targets:

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Promoter	Log-likelihood	Transcript	Gene	Gene Info
chr1_+_80321585 Show fit	46.62	ENSRNOT00000022895	Ckm NCBI RGD Ensembl Show fit	creatine kinase, M-type
chr10_+_110631494 Show fit	35.04	ENSRNOT00000054915	Fn3k NCBI RGD Ensembl Show fit	fructosamine 3 kinase
chr13_+_85818427 Show fit	31.81	ENSRNOT00000077227 ENSRNOT00000006117	Rxrg NCBI RGD Ensembl Show fit	retinoid X receptor gamma
chr1_+_101161252 Show fit	28.03	ENSRNOT00000028064 ENSRNOT00000064184	Slc17a7 NCBI RGD Ensembl Show fit	solute carrier family 17 member 7
chr15_+_34251606 Show fit	26.98	ENSRNOT00000025725	Fitm1 NCBI RGD Ensembl Show fit	fat storage-inducing transmembrane protein 1
chr3_-_2534375 Show fit	25.25	ENSRNOT00000037725	Grin1 NCBI RGD Ensembl Show fit	glutamate ionotropic receptor NMDA type subunit 1
chr15_+_43905099 Show fit	24.46	ENSRNOT00000016568	Ebf2 NCBI RGD Ensembl Show fit	early B-cell factor 2
chr4_-_85915099 Show fit	22.92	ENSRNOT00000016182	Neurod6 NCBI RGD Ensembl Show fit	neuronal differentiation 6
chr16_+_46731403 Show fit	22.75	ENSRNOT00000017624	Tenm3 NCBI RGD Ensembl Show fit	teneurin transmembrane protein 3
chr4_-_129619142 Show fit	20.67	ENSRNOT00000047453	Lmod3 NCBI RGD Ensembl Show fit	leiomodin 3

Showing 1 to 10 of 200 entries

Network of associatons between targets according to the STRING database.

First level regulatory network of Neurod1

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Gene Ontology Analysis

Gene overrepresentation in biological process category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.4	507.9	GO:0050911	detection of chemical stimulus involved in sensory perception of smell(GO:0050911)
0.7	42.4	GO:0042398	cellular modified amino acid biosynthetic process(GO:0042398)
12.9	38.8	GO:1900673	olefin metabolic process(GO:1900673)
0.9	35.0	GO:0006040	amino sugar metabolic process(GO:0006040)
1.1	31.8	GO:1901522	positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus(GO:1901522)
7.0	28.0	GO:0097401	synaptic vesicle lumen acidification(GO:0097401)
3.9	27.0	GO:0010890	positive regulation of sequestering of triglyceride(GO:0010890)
0.6	25.3	GO:0007026	negative regulation of microtubule depolymerization(GO:0007026)
1.9	24.5	GO:0035563	positive regulation of chromatin binding(GO:0035563)
1.1	22.9	GO:0021542	dentate gyrus development(GO:0021542)

Showing 1 to 10 of 117 entries

Gene overrepresentation in cellular component category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.1	379.6	GO:0016021	integral component of membrane(GO:0016021)
4.6	45.8	GO:0044300	cerebellar mossy fiber(GO:0044300)
2.4	45.1	GO:0016010	dystrophin-associated glycoprotein complex(GO:0016010) glycoprotein complex(GO:0090665)
9.7	38.8	GO:0044307	dendritic branch(GO:0044307)
0.6	33.5	GO:0031672	A band(GO:0031672)
0.1	26.5	GO:0031965	nuclear membrane(GO:0031965)
0.5	20.6	GO:0044295	axonal growth cone(GO:0044295)
1.0	20.5	GO:0030285	integral component of synaptic vesicle membrane(GO:0030285) intrinsic component of synaptic vesicle membrane(GO:0098563)
2.5	19.9	GO:0045261	mitochondrial proton-transporting ATP synthase complex, catalytic core F(1)(GO:0000275) proton-transporting ATP synthase complex, catalytic core F(1)(GO:0045261)
1.3	19.2	GO:0017146	NMDA selective glutamate receptor complex(GO:0017146)

Showing 1 to 10 of 60 entries

Gene overrepresentation in molecular function category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.4	507.9	GO:0004984	olfactory receptor activity(GO:0004984)
6.7	46.6	GO:0004111	creatine kinase activity(GO:0004111)
7.8	38.8	GO:1904315	transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential(GO:1904315)
0.1	32.6	GO:0001077	transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding(GO:0001077)
5.3	31.8	GO:0004886	9-cis retinoic acid receptor activity(GO:0004886)
5.6	28.0	GO:0015321	inorganic phosphate transmembrane transporter activity(GO:0005315) sodium-dependent phosphate transmembrane transporter activity(GO:0015321)
0.7	24.6	GO:0001106	RNA polymerase II transcription corepressor activity(GO:0001106)
1.6	24.5	GO:0005523	tropomyosin binding(GO:0005523)
0.2	22.1	GO:0005262	calcium channel activity(GO:0005262)
0.7	20.5	GO:0017075	syntaxin-1 binding(GO:0017075)

Showing 1 to 10 of 90 entries

Gene overrepresentation in curated gene sets: canonical pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.6	25.2	SIG CD40PATHWAYMAP	Genes related to CD40 signaling
0.7	23.5	PID RETINOIC ACID PATHWAY	Retinoic acid receptors-mediated signaling
0.8	19.2	PID PDGFRA PATHWAY	PDGFR-alpha signaling pathway
0.4	17.8	PID HNF3A PATHWAY	FOXA1 transcription factor network
0.5	15.1	PID MAPK TRK PATHWAY	Trk receptor signaling mediated by the MAPK pathway
0.5	14.6	PID P38 MKK3 6PATHWAY	p38 MAPK signaling pathway
0.5	14.4	PID INSULIN GLUCOSE PATHWAY	Insulin-mediated glucose transport
0.3	13.2	PID CERAMIDE PATHWAY	Ceramide signaling pathway
0.4	12.6	PID MYC PATHWAY	C-MYC pathway
0.2	10.9	PID RB 1PATHWAY	Regulation of retinoblastoma protein

Showing 1 to 10 of 17 entries

Gene overrepresentation in curated gene sets: REACTOME pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
2.1	47.2	REACTOME GLUTAMATE NEUROTRANSMITTER RELEASE CYCLE	Genes involved in Glutamate Neurotransmitter Release Cycle
0.2	44.8	REACTOME METABOLISM OF AMINO ACIDS AND DERIVATIVES	Genes involved in Metabolism of amino acids and derivatives
0.6	41.0	REACTOME NUCLEAR RECEPTOR TRANSCRIPTION PATHWAY	Genes involved in Nuclear Receptor transcription pathway
2.2	38.8	REACTOME CREB PHOSPHORYLATION THROUGH THE ACTIVATION OF CAMKII	Genes involved in CREB phosphorylation through the activation of CaMKII
0.6	23.6	REACTOME STRIATED MUSCLE CONTRACTION	Genes involved in Striated Muscle Contraction
1.2	19.9	REACTOME FORMATION OF ATP BY CHEMIOSMOTIC COUPLING	Genes involved in Formation of ATP by chemiosmotic coupling
0.8	17.8	REACTOME RNA POL III TRANSCRIPTION TERMINATION	Genes involved in RNA Polymerase III Transcription Termination
0.4	15.9	REACTOME GLYCOLYSIS	Genes involved in Glycolysis
1.7	15.3	REACTOME TETRAHYDROBIOPTERIN BH4 SYNTHESIS RECYCLING SALVAGE AND REGULATION	Genes involved in Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation
0.3	14.9	REACTOME NCAM1 INTERACTIONS	Genes involved in NCAM1 interactions

Showing 1 to 10 of 27 entries

Results for Neurod1

Z-value: 1.29

Motif logo

Transcription factors associated with Neurod1

Activity-expression correlation:

Activity profile of Neurod1 motif

Sorted Z-values of Neurod1 motif

Top targets:

Network of associatons between targets according to the STRING database.

First level regulatory network of Neurod1

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Gene Ontology Analysis

Gene overrepresentation in biological process category:

Gene overrepresentation in cellular component category:

Gene overrepresentation in molecular function category:

Gene overrepresentation in curated gene sets: canonical pathways category:

Gene overrepresentation in curated gene sets: REACTOME pathways category: