ISMARA results: Hoxa4

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GSE53960: rat RNA-Seq transcriptomic Bodymap

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Results for Hoxa4

Z-value: 1.50

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Transcription factors associated with Hoxa4

Gene Symbol	Gene ID	Gene Info
Hoxa4 NCBI RGD Ensembl	ENSRNOG00000027365	homeo box A4

Activity-expression correlation:

Gene	Promoter	Pearson corr. coef.	P-value	Plot
Hoxa4	rn6_v1_chr4_-_82160240_82160240	0.06	2.9e-01	Click!

Activity profile of Hoxa4 motif

Sorted Z-values of Hoxa4 motif

Top targets:

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Promoter	Log-likelihood	Transcript	Gene	Gene Info
chr3_-_63836017 Show fit	127.06	ENSRNOT00000030978	AABR07052585.1 NCBI RGD Ensembl Show fit
chr12_+_49761120 Show fit	78.12	ENSRNOT00000070961	Myo18b NCBI RGD Ensembl Show fit	myosin XVIIIb
chr11_+_66713888 Show fit	76.43	ENSRNOT00000003340	Fbxo40 NCBI RGD Ensembl Show fit	F-box protein 40
chr10_+_53740841 Show fit	65.70	ENSRNOT00000004295	Myh2 NCBI RGD Ensembl Show fit	myosin heavy chain 2
chr15_-_27819376 Show fit	63.01	ENSRNOT00000067400	A930018M24Rik NCBI RGD Ensembl Show fit	RIKEN cDNA A930018M24 gene
chr8_-_130429132 Show fit	62.93	ENSRNOT00000026261	Hhatl NCBI RGD Ensembl Show fit	hedgehog acyltransferase-like
chr13_+_52889737 Show fit	56.35	ENSRNOT00000074366	Cacna1s NCBI RGD Ensembl Show fit	calcium voltage-gated channel subunit alpha1 S
chr10_+_53818818 Show fit	54.67	ENSRNOT00000057260	Myh8 NCBI RGD Ensembl Show fit	myosin heavy chain 8
chr10_+_53778662 Show fit	52.75	ENSRNOT00000045718	Myh2 NCBI RGD Ensembl Show fit	myosin heavy chain 2
chr4_-_15859132 Show fit	51.63	ENSRNOT00000082161	Cacna2d1 NCBI RGD Ensembl Show fit	calcium voltage-gated channel auxiliary subunit alpha2delta 1

Showing 1 to 10 of 174 entries

Network of associatons between targets according to the STRING database.

First level regulatory network of Hoxa4

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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
9.1	118.5	GO:0001778	plasma membrane repair(GO:0001778)
6.7	79.9	GO:0048739	cardiac muscle fiber development(GO:0048739)
10.5	62.9	GO:1903059	regulation of protein lipidation(GO:1903059)
8.0	56.3	GO:0002074	extraocular skeletal muscle development(GO:0002074)
0.4	55.6	GO:0007156	homophilic cell adhesion via plasma membrane adhesion molecules(GO:0007156)
6.1	54.7	GO:0030049	muscle filament sliding(GO:0030049)
8.6	51.6	GO:1901843	membrane depolarization during bundle of His cell action potential(GO:0086048) positive regulation of high voltage-gated calcium channel activity(GO:1901843)
2.5	43.0	GO:2001014	regulation of skeletal muscle cell differentiation(GO:2001014)
6.1	42.4	GO:0014816	skeletal muscle satellite cell differentiation(GO:0014816) negative regulation of skeletal muscle cell differentiation(GO:2001015)
2.2	38.1	GO:0051386	regulation of neurotrophin TRK receptor signaling pathway(GO:0051386)

Showing 1 to 10 of 89 entries

Gene overrepresentation in cellular component category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.0	249.0	GO:0016021	integral component of membrane(GO:0016021)
13.2	118.5	GO:0005826	actomyosin contractile ring(GO:0005826)
0.6	88.7	GO:0030018	Z disc(GO:0030018)
8.7	78.1	GO:0016461	unconventional myosin complex(GO:0016461)
1.7	56.3	GO:0005891	voltage-gated calcium channel complex(GO:0005891)
3.9	54.7	GO:0032982	myosin filament(GO:0032982)
0.2	43.0	GO:0005802	trans-Golgi network(GO:0005802)
0.8	39.0	GO:0005747	mitochondrial respiratory chain complex I(GO:0005747) NADH dehydrogenase complex(GO:0030964) respiratory chain complex I(GO:0045271)
0.1	30.4	GO:0030427	site of polarized growth(GO:0030427)
2.5	29.5	GO:1990454	L-type voltage-gated calcium channel complex(GO:1990454)

Showing 1 to 10 of 44 entries

Gene overrepresentation in molecular function category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.3	132.9	GO:0003779	actin binding(GO:0003779)
0.6	77.9	GO:0003774	motor activity(GO:0003774)
0.3	76.4	GO:0061630	ubiquitin protein ligase activity(GO:0061630)
2.5	54.7	GO:0000146	microfilament motor activity(GO:0000146)
17.2	51.6	GO:0086057	voltage-gated calcium channel activity involved in bundle of His cell action potential(GO:0086057)
0.8	44.2	GO:0005160	transforming growth factor beta receptor binding(GO:0005160)
1.4	38.5	GO:0050136	NADH dehydrogenase (ubiquinone) activity(GO:0008137) NADH dehydrogenase (quinone) activity(GO:0050136)
0.1	34.9	GO:0044822	mRNA binding(GO:0003729) poly(A) RNA binding(GO:0044822)
1.8	34.2	GO:0008331	high voltage-gated calcium channel activity(GO:0008331)
4.9	34.0	GO:0070095	fructose-6-phosphate binding(GO:0070095)

Showing 1 to 10 of 77 entries

Gene overrepresentation in curated gene sets: canonical pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
2.6	118.5	PID INTEGRIN A4B1 PATHWAY	Alpha4 beta1 integrin signaling events
0.2	65.6	NABA SECRETED FACTORS	Genes encoding secreted soluble factors
0.1	31.3	NABA ECM REGULATORS	Genes encoding enzymes and their regulators involved in the remodeling of the extracellular matrix
0.7	29.1	PID RET PATHWAY	Signaling events regulated by Ret tyrosine kinase
0.2	18.7	PID MYC ACTIV PATHWAY	Validated targets of C-MYC transcriptional activation
0.1	18.4	NABA MATRISOME ASSOCIATED	Ensemble of genes encoding ECM-associated proteins including ECM-affilaited proteins, ECM regulators and secreted factors
0.3	15.0	PID BMP PATHWAY	BMP receptor signaling
0.3	11.3	PID EPHA FWDPATHWAY	EPHA forward signaling
0.1	10.3	PID P53 DOWNSTREAM PATHWAY	Direct p53 effectors
0.3	8.4	PID CONE PATHWAY	Visual signal transduction: Cones

Showing 1 to 10 of 14 entries

Gene overrepresentation in curated gene sets: REACTOME pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
1.3	56.3	REACTOME NCAM1 INTERACTIONS	Genes involved in NCAM1 interactions
1.4	54.7	REACTOME STRIATED MUSCLE CONTRACTION	Genes involved in Striated Muscle Contraction
0.9	34.0	REACTOME GLYCOLYSIS	Genes involved in Glycolysis
0.3	28.8	REACTOME CLASS B 2 SECRETIN FAMILY RECEPTORS	Genes involved in Class B/2 (Secretin family receptors)
0.8	24.5	REACTOME TRANSFERRIN ENDOCYTOSIS AND RECYCLING	Genes involved in Transferrin endocytosis and recycling
0.3	21.1	REACTOME RESPIRATORY ELECTRON TRANSPORT	Genes involved in Respiratory electron transport
0.6	18.7	REACTOME SYNTHESIS OF PA	Genes involved in Synthesis of PA
0.8	15.2	REACTOME ABCA TRANSPORTERS IN LIPID HOMEOSTASIS	Genes involved in ABCA transporters in lipid homeostasis
0.4	12.5	REACTOME ADHERENS JUNCTIONS INTERACTIONS	Genes involved in Adherens junctions interactions
0.2	9.0	REACTOME SPHINGOLIPID DE NOVO BIOSYNTHESIS	Genes involved in Sphingolipid de novo biosynthesis

Showing 1 to 10 of 20 entries

Results for Hoxa4

Z-value: 1.50

Motif logo

Transcription factors associated with Hoxa4

Activity-expression correlation:

Activity profile of Hoxa4 motif

Sorted Z-values of Hoxa4 motif

Top targets:

Network of associatons between targets according to the STRING database.

First level regulatory network of Hoxa4

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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: