ISMARA results: Myod1

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GSE53960: rat RNA-Seq transcriptomic Bodymap

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Results for Myod1

Z-value: 1.53

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Transcription factors associated with Myod1

Gene Symbol	Gene ID	Gene Info
Myod1 NCBI RGD Ensembl	ENSRNOG00000011306	myogenic differentiation 1

Activity-expression correlation:

Gene	Promoter	Pearson corr. coef.	P-value	Plot
Myod1	rn6_v1_chr1_+_102396538_102396538	0.65	2.5e-39	Click!

Activity profile of Myod1 motif

Sorted Z-values of Myod1 motif

Top targets:

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Promoter	Log-likelihood	Transcript	Gene	Gene Info
chr1_+_80321585 Show fit	128.20	ENSRNOT00000022895	Ckm NCBI RGD Ensembl Show fit	creatine kinase, M-type
chr3_-_72219246 Show fit	121.12	ENSRNOT00000009903	Smtnl1 NCBI RGD Ensembl Show fit	smoothelin-like 1
chr1_+_198655742 Show fit	108.42	ENSRNOT00000023944	Mylpf NCBI RGD Ensembl Show fit	myosin light chain, phosphorylatable, fast skeletal muscle
chr1_+_215609036 Show fit	100.95	ENSRNOT00000076187	Tnni2 NCBI RGD Ensembl Show fit	troponin I2, fast skeletal type
chr5_-_59025631 Show fit	97.23	ENSRNOT00000049000 ENSRNOT00000022801	Tpm2 NCBI RGD Ensembl Show fit	tropomyosin 2, beta
chr3_+_148386189 Show fit	96.11	ENSRNOT00000011255	Mylk2 NCBI RGD Ensembl Show fit	myosin light chain kinase 2
chr10_+_70262361 Show fit	95.64	ENSRNOT00000064625 ENSRNOT00000076973	Unc45b NCBI RGD Ensembl Show fit	unc-45 myosin chaperone B
chr1_-_80331626 Show fit	89.65	ENSRNOT00000022577	AABR07002677.1 NCBI RGD Ensembl Show fit
chr15_+_34251606 Show fit	86.39	ENSRNOT00000025725	Fitm1 NCBI RGD Ensembl Show fit	fat storage-inducing transmembrane protein 1
chr8_+_130416355 Show fit	81.92	ENSRNOT00000026234	Klhl40 NCBI RGD Ensembl Show fit	kelch-like family member 40

Showing 1 to 10 of 200 entries

Network of associatons between targets according to the STRING database.

First level regulatory network of Myod1

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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
5.3	244.7	GO:0003009	skeletal muscle contraction(GO:0003009)
2.2	133.3	GO:0042398	cellular modified amino acid biosynthetic process(GO:0042398)
2.0	114.8	GO:0043462	regulation of ATPase activity(GO:0043462)
2.1	113.8	GO:0045907	positive regulation of vasoconstriction(GO:0045907)
0.7	102.9	GO:0007519	skeletal muscle tissue development(GO:0007519)
32.0	96.1	GO:0031448	regulation of fast-twitch skeletal muscle fiber contraction(GO:0031446) positive regulation of fast-twitch skeletal muscle fiber contraction(GO:0031448)
12.0	95.9	GO:0051694	pointed-end actin filament capping(GO:0051694)
1.4	95.6	GO:0061077	chaperone-mediated protein folding(GO:0061077)
12.3	86.4	GO:0010890	positive regulation of sequestering of triglyceride(GO:0010890)
16.4	81.9	GO:0098528	skeletal muscle fiber differentiation(GO:0098528)

Showing 1 to 10 of 102 entries

Gene overrepresentation in cellular component category:

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Log-likelihood per target	Total log-likelihood	Term	Description
5.5	307.3	GO:0031672	A band(GO:0031672)
12.3	147.6	GO:0005861	troponin complex(GO:0005861)
2.9	130.1	GO:0005891	voltage-gated calcium channel complex(GO:0005891)
18.1	126.6	GO:0005862	muscle thin filament tropomyosin(GO:0005862)
1.7	99.4	GO:0016459	myosin complex(GO:0016459)
0.7	91.5	GO:0030017	sarcomere(GO:0030017)
0.6	78.9	GO:0030176	integral component of endoplasmic reticulum membrane(GO:0030176)
15.5	77.6	GO:0045098	type III intermediate filament(GO:0045098)
3.6	72.3	GO:0001518	voltage-gated sodium channel complex(GO:0001518)
3.6	71.9	GO:0005892	acetylcholine-gated channel complex(GO:0005892)

Showing 1 to 10 of 54 entries

Gene overrepresentation in molecular function category:

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Log-likelihood per target	Total log-likelihood	Term	Description
5.5	254.1	GO:0008307	structural constituent of muscle(GO:0008307)
12.0	191.7	GO:0005523	tropomyosin binding(GO:0005523)
24.7	172.9	GO:0031014	troponin T binding(GO:0031014)
18.3	128.2	GO:0004111	creatine kinase activity(GO:0004111)
24.0	96.1	GO:0004687	myosin light chain kinase activity(GO:0004687)
2.2	88.9	GO:0051879	Hsp90 protein binding(GO:0051879)
13.6	81.4	GO:0004126	cytidine deaminase activity(GO:0004126)
0.2	73.9	GO:0004842	ubiquitin-protein transferase activity(GO:0004842)
2.4	72.3	GO:0005248	voltage-gated sodium channel activity(GO:0005248) voltage-gated ion channel activity involved in regulation of postsynaptic membrane potential(GO:1905030)
4.2	71.9	GO:0022848	acetylcholine-gated cation channel activity(GO:0022848)

Showing 1 to 10 of 72 entries

Gene overrepresentation in curated gene sets: canonical pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
1.7	143.5	PID RB 1PATHWAY	Regulation of retinoblastoma protein
0.8	102.8	PID ERBB1 DOWNSTREAM PATHWAY	ErbB1 downstream signaling
2.0	96.1	SIG REGULATION OF THE ACTIN CYTOSKELETON BY RHO GTPASES	Genes related to regulation of the actin cytoskeleton
1.4	63.7	PID AURORA B PATHWAY	Aurora B signaling
0.1	26.6	NABA ECM REGULATORS	Genes encoding enzymes and their regulators involved in the remodeling of the extracellular matrix
1.0	26.4	PID ERBB2 ERBB3 PATHWAY	ErbB2/ErbB3 signaling events
0.5	23.4	PID HEDGEHOG GLI PATHWAY	Hedgehog signaling events mediated by Gli proteins
1.1	23.2	PID INTEGRIN5 PATHWAY	Beta5 beta6 beta7 and beta8 integrin cell surface interactions
0.6	21.6	PID FOXO PATHWAY	FoxO family signaling
0.3	15.0	PID AJDISS 2PATHWAY	Posttranslational regulation of adherens junction stability and dissassembly

Showing 1 to 10 of 26 entries

Gene overrepresentation in curated gene sets: REACTOME pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
10.5	409.4	REACTOME STRIATED MUSCLE CONTRACTION	Genes involved in Striated Muscle Contraction
0.6	118.6	REACTOME METABOLISM OF AMINO ACIDS AND DERIVATIVES	Genes involved in Metabolism of amino acids and derivatives
3.0	106.6	REACTOME INTERACTION BETWEEN L1 AND ANKYRINS	Genes involved in Interaction between L1 and Ankyrins
6.0	71.9	REACTOME PRESYNAPTIC NICOTINIC ACETYLCHOLINE RECEPTORS	Genes involved in Presynaptic nicotinic acetylcholine receptors
0.4	70.1	REACTOME ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION	Genes involved in Antigen processing: Ubiquitination & Proteasome degradation
1.5	63.0	REACTOME NCAM1 INTERACTIONS	Genes involved in NCAM1 interactions
2.4	47.8	REACTOME GLYCOGEN BREAKDOWN GLYCOGENOLYSIS	Genes involved in Glycogen breakdown (glycogenolysis)
1.4	35.4	REACTOME ERK MAPK TARGETS	Genes involved in ERK/MAPK targets
0.2	14.1	REACTOME LOSS OF NLP FROM MITOTIC CENTROSOMES	Genes involved in Loss of Nlp from mitotic centrosomes
0.3	12.7	REACTOME COLLAGEN FORMATION	Genes involved in Collagen formation

Showing 1 to 10 of 29 entries

Results for Myod1

Z-value: 1.53

Motif logo

Transcription factors associated with Myod1

Activity-expression correlation:

Activity profile of Myod1 motif

Sorted Z-values of Myod1 motif

Top targets:

Network of associatons between targets according to the STRING database.

First level regulatory network of Myod1

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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: