ISMARA results: Hoxc4_Arx_Otp_Esx1

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GSE49485: Hypoxia transcriptome sequencing of rat brain.

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Results for Hoxc4_Arx_Otp_Esx1_Phox2b

Z-value: 0.92

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Transcription factors associated with Hoxc4_Arx_Otp_Esx1_Phox2b

Gene Symbol	Gene ID	Gene Info
Hoxc4 NCBI RGD Ensembl	ENSRNOG00000016613	homeo box C4
Arx NCBI RGD Ensembl	ENSRNOG00000053562	aristaless related homeobox
Otp NCBI RGD Ensembl	ENSRNOG00000010560	orthopedia homeobox
Esx1 NCBI RGD Ensembl	ENSRNOG00000048011	ESX homeobox 1
Phox2b NCBI RGD Ensembl	ENSRNOG00000051929	paired-like homeobox 2b

Activity-expression correlation:

Gene	Promoter	Pearson corr. coef.	P-value	Plot
Arx	rn6_v1_chrX_+_62363953_62363953	0.95	1.2e-02	Click!
Otp	rn6_v1_chr2_+_24546536_24546536	0.38	5.2e-01	Click!
Hoxc4	rn6_v1_chr7_+_144647587_144647587	0.23	7.1e-01	Click!
Phox2b	rn6_v1_chr14_+_42714315_42714315	0.10	8.7e-01	Click!

Activity profile of Hoxc4_Arx_Otp_Esx1_Phox2b motif

Sorted Z-values of Hoxc4_Arx_Otp_Esx1_Phox2b motif

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Promoter	Log-likelihood	Transcript	Gene	Gene Info
chr12_-_2174131 Show fit	2.26	ENSRNOT00000001313	Pcp2 NCBI RGD Ensembl Show fit	Purkinje cell protein 2
chr1_-_190370499 Show fit	1.35	ENSRNOT00000084389	AABR07005618.1 NCBI RGD Ensembl Show fit
chr10_-_88670430 Show fit	1.12	ENSRNOT00000025547	Hcrt NCBI RGD Ensembl Show fit	hypocretin neuropeptide precursor
chrX_+_144994139 Show fit	0.83	ENSRNOT00000071783	LOC102546596 NCBI RGD Ensembl Show fit	pre-mRNA-splicing factor CWC22 homolog
chr2_+_127525285 Show fit	0.83	ENSRNOT00000093247	Intu NCBI RGD Ensembl Show fit	inturned planar cell polarity protein
chr15_+_37790141 Show fit	0.72	ENSRNOT00000076392 ENSRNOT00000091953	Il17d NCBI RGD Ensembl Show fit	interleukin 17D
chr4_+_169161585 Show fit	0.61	ENSRNOT00000079785	Emp1 NCBI RGD Ensembl Show fit	epithelial membrane protein 1
chrX_-_40086870 Show fit	0.59	ENSRNOT00000010027	Smpx NCBI RGD Ensembl Show fit	small muscle protein, X-linked
chr2_+_158097843 Show fit	0.56	ENSRNOT00000016541	Ptx3 NCBI RGD Ensembl Show fit	pentraxin 3
chr10_+_61685645 Show fit	0.48	ENSRNOT00000003933	Mnt NCBI RGD Ensembl Show fit	MAX network transcriptional repressor

Showing 1 to 10 of 200 entries

Network of associatons between targets according to the STRING database.

First level regulatory network of Hoxc4_Arx_Otp_Esx1_Phox2b

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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
0.3	2.0	GO:0016056	rhodopsin mediated signaling pathway(GO:0016056)
0.2	1.1	GO:0051970	negative regulation of transmission of nerve impulse(GO:0051970)
0.1	0.9	GO:0032060	bleb assembly(GO:0032060)
0.2	0.6	GO:0052422	modulation of catalytic activity in other organism involved in symbiotic interaction(GO:0052203) modulation by host of symbiont catalytic activity(GO:0052422) regulation of exo-alpha-sialidase activity(GO:1903015)
0.0	0.5	GO:0010839	negative regulation of keratinocyte proliferation(GO:0010839)
0.1	0.3	GO:0007468	regulation of rhodopsin gene expression(GO:0007468)
0.1	0.3	GO:0098886	modification of dendritic spine(GO:0098886)
0.0	0.3	GO:2000323	negative regulation of glucocorticoid receptor signaling pathway(GO:2000323)
0.1	0.2	GO:0021886	cerebral cortex tangential migration using cell-axon interactions(GO:0021824) gonadotrophin-releasing hormone neuronal migration to the hypothalamus(GO:0021828) hypothalamic tangential migration using cell-axon interactions(GO:0021856) hypothalamus gonadotrophin-releasing hormone neuron differentiation(GO:0021886) hypothalamus gonadotrophin-releasing hormone neuron development(GO:0021888) facioacoustic ganglion development(GO:1903375)
0.0	0.2	GO:0034475	U4 snRNA 3'-end processing(GO:0034475) DNA deamination(GO:0045006) polyadenylation-dependent snoRNA 3'-end processing(GO:0071051)

Showing 1 to 10 of 39 entries

Gene overrepresentation in cellular component category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.1	0.6	GO:0005927	muscle tendon junction(GO:0005927)
0.1	0.3	GO:0097444	spine apparatus(GO:0097444)
0.0	0.3	GO:0005726	perichromatin fibrils(GO:0005726)
0.0	0.3	GO:0000177	cytoplasmic exosome (RNase complex)(GO:0000177)
0.0	0.2	GO:0000408	EKC/KEOPS complex(GO:0000408)
0.0	0.2	GO:0034709	methylosome(GO:0034709)
0.0	0.2	GO:0005666	DNA-directed RNA polymerase III complex(GO:0005666)
0.0	0.1	GO:0032398	MHC class Ib protein complex(GO:0032398)
0.0	0.1	GO:0042585	germinal vesicle(GO:0042585) dendritic branch(GO:0044307)
0.0	0.1	GO:0099571	postsynaptic actin cytoskeleton(GO:0098871) postsynaptic cytoskeleton(GO:0099571)

Showing 1 to 10 of 15 entries

Gene overrepresentation in molecular function category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.0	1.1	GO:0005184	neuropeptide hormone activity(GO:0005184)
0.1	0.4	GO:0004065	arylsulfatase activity(GO:0004065)
0.0	0.4	GO:0017081	chloride channel regulator activity(GO:0017081)
0.1	0.3	GO:0001849	complement component C1q binding(GO:0001849)
0.0	0.3	GO:0030215	semaphorin receptor binding(GO:0030215)
0.0	0.3	GO:0043522	leucine zipper domain binding(GO:0043522)
0.1	0.2	GO:0070996	type 1 melanocortin receptor binding(GO:0070996)
0.0	0.2	GO:0008327	methyl-CpG binding(GO:0008327)
0.0	0.1	GO:0008940	nitrate reductase activity(GO:0008940)
0.0	0.1	GO:1990932	5.8S rRNA binding(GO:1990932)

Showing 1 to 10 of 19 entries

Gene overrepresentation in curated gene sets: canonical pathways category:

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Total log-likelihood	Term	Description
0.5	ST ADRENERGIC	Adrenergic Pathway
0.3	PID SYNDECAN 3 PATHWAY	Syndecan-3-mediated signaling events
0.3	PID CIRCADIAN PATHWAY	Circadian rhythm pathway

Showing 1 to 3 of 3 entries

Gene overrepresentation in curated gene sets: REACTOME pathways category:

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Total log-likelihood	Term	Description
0.4	REACTOME THE ACTIVATION OF ARYLSULFATASES	Genes involved in The activation of arylsulfatases
0.3	REACTOME PEPTIDE HORMONE BIOSYNTHESIS	Genes involved in Peptide hormone biosynthesis
0.2	REACTOME CRMPS IN SEMA3A SIGNALING	Genes involved in CRMPs in Sema3A signaling
0.2	REACTOME MRNA DECAY BY 3 TO 5 EXORIBONUCLEASE	Genes involved in mRNA Decay by 3' to 5' Exoribonuclease
0.1	REACTOME SYNTHESIS OF PIPS AT THE LATE ENDOSOME MEMBRANE	Genes involved in Synthesis of PIPs at the late endosome membrane
0.1	REACTOME REGULATION OF INSULIN SECRETION BY ACETYLCHOLINE	Genes involved in Regulation of Insulin Secretion by Acetylcholine
0.1	REACTOME ROLE OF DCC IN REGULATING APOPTOSIS	Genes involved in Role of DCC in regulating apoptosis

Showing 1 to 7 of 7 entries

Results for Hoxc4_Arx_Otp_Esx1_Phox2b

Z-value: 0.92

Motif logo

Transcription factors associated with Hoxc4_Arx_Otp_Esx1_Phox2b

Activity-expression correlation:

Activity profile of Hoxc4_Arx_Otp_Esx1_Phox2b motif

Sorted Z-values of Hoxc4_Arx_Otp_Esx1_Phox2b motif

Top targets:

Network of associatons between targets according to the STRING database.

First level regulatory network of Hoxc4_Arx_Otp_Esx1_Phox2b

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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: