ISMARA results: Ybx1_Nfya_Nfyb_Nfyc

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GSE49485: Hypoxia transcriptome sequencing of rat brain.

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Results for Ybx1_Nfya_Nfyb_Nfyc_Cebpz

Z-value: 2.65

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Transcription factors associated with Ybx1_Nfya_Nfyb_Nfyc_Cebpz

Gene Symbol	Gene ID	Gene Info
Ybx1 NCBI RGD Ensembl	ENSRNOG00000023786	Y box binding protein 1
Nfya NCBI RGD Ensembl	ENSRNOG00000012702	nuclear transcription factor Y subunit alpha
Nfyb NCBI RGD Ensembl	ENSRNOG00000010309	nuclear transcription factor Y subunit beta
Nfyc NCBI RGD Ensembl	ENSRNOG00000010735	nuclear transcription factor Y subunit gamma
Cebpz NCBI RGD Ensembl	ENSRNOG00000005087	CCAAT/enhancer binding protein zeta

Activity-expression correlation:

Gene	Promoter	Pearson corr. coef.	P-value	Plot
Nfyb	rn6_v1_chr7_+_27081667_27081667	-0.76	1.3e-01	Click!
Cebpz	rn6_v1_chr6_-_1534488_1534488	-0.75	1.5e-01	Click!
Nfya	rn6_v1_chr9_+_14551758_14551758	-0.60	2.9e-01	Click!
Ybx1	rn6_v1_chr5_-_138336475_138336475	0.45	4.5e-01	Click!
Nfyc	rn6_v1_chr5_-_139749050_139749050	0.44	4.6e-01	Click!

Activity profile of Ybx1_Nfya_Nfyb_Nfyc_Cebpz motif

Sorted Z-values of Ybx1_Nfya_Nfyb_Nfyc_Cebpz motif

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Promoter	Log-likelihood	Transcript	Gene	Gene Info
chr10_+_105393072 Show fit	2.56	ENSRNOT00000013359	Ubald2 NCBI RGD Ensembl Show fit	UBA-like domain containing 2
chr2_-_198382190 Show fit	2.35	ENSRNOT00000044268	Hist2h2aa2 NCBI RGD Ensembl Show fit	histone cluster 2, H2aa2
chr2_+_198388809 Show fit	2.30	ENSRNOT00000083087	Hist2h2aa3 NCBI RGD Ensembl Show fit	histone cluster 2, H2aa3
chr10_-_15577977 Show fit	2.14	ENSRNOT00000052292	Hba-a3 NCBI RGD Ensembl Show fit	hemoglobin alpha, adult chain 3
chr2_+_198359754 Show fit	1.96	ENSRNOT00000048582	Hist2h2ab NCBI RGD Ensembl Show fit	histone cluster 2 H2A family member b
chr3_-_9037942 Show fit	1.89	ENSRNOT00000036770	Ier5l NCBI RGD Ensembl Show fit	immediate early response 5-like
chr10_-_15590220 Show fit	1.66	ENSRNOT00000048977	Hba-a2 NCBI RGD Ensembl Show fit	hemoglobin alpha, adult chain 2
chr2_-_198360678 Show fit	1.66	ENSRNOT00000051917	Hist2h2ac NCBI RGD Ensembl Show fit	histone cluster 2 H2A family member c
chr10_-_15603649 Show fit	1.55	ENSRNOT00000051483	Hba-a2 NCBI RGD Ensembl Show fit	hemoglobin alpha, adult chain 2
chr1_-_216663720 Show fit	1.55	ENSRNOT00000078944 ENSRNOT00000077409	Cdkn1c NCBI RGD Ensembl Show fit	cyclin-dependent kinase inhibitor 1C

Showing 1 to 10 of 200 entries

Network of associatons between targets according to the STRING database.

First level regulatory network of Ybx1_Nfya_Nfyb_Nfyc_Cebpz

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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
0.1	11.7	GO:0006342	chromatin silencing(GO:0006342)
0.6	6.8	GO:0015671	oxygen transport(GO:0015671)
0.1	4.0	GO:0006334	nucleosome assembly(GO:0006334)
0.1	2.9	GO:0006335	DNA replication-dependent nucleosome assembly(GO:0006335) DNA replication-dependent nucleosome organization(GO:0034723)
0.2	2.4	GO:0002227	innate immune response in mucosa(GO:0002227)
0.1	2.0	GO:0045475	locomotor rhythm(GO:0045475)
0.1	1.8	GO:0071712	ER-associated misfolded protein catabolic process(GO:0071712)
0.3	1.7	GO:1902746	regulation of lens fiber cell differentiation(GO:1902746)
0.2	1.7	GO:1904153	negative regulation of protein exit from endoplasmic reticulum(GO:0070862) negative regulation of retrograde protein transport, ER to cytosol(GO:1904153)
0.1	1.7	GO:0000185	activation of MAPKKK activity(GO:0000185)

Showing 1 to 10 of 401 entries

Gene overrepresentation in cellular component category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.3	24.3	GO:0000786	nucleosome(GO:0000786)
0.5	5.6	GO:0034663	endoplasmic reticulum chaperone complex(GO:0034663)
1.0	4.0	GO:0031838	haptoglobin-hemoglobin complex(GO:0031838)
0.6	2.8	GO:0005833	hemoglobin complex(GO:0005833)
0.0	2.8	GO:0043209	myelin sheath(GO:0043209)
0.0	2.0	GO:0005884	actin filament(GO:0005884)
0.1	1.8	GO:0042612	MHC class I protein complex(GO:0042612)
0.3	1.7	GO:0005785	signal recognition particle receptor complex(GO:0005785)
0.1	1.7	GO:0019028	viral nucleocapsid(GO:0019013) viral capsid(GO:0019028)
0.1	1.5	GO:0005680	anaphase-promoting complex(GO:0005680)

Showing 1 to 10 of 173 entries

Gene overrepresentation in molecular function category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.0	16.4	GO:0046982	protein heterodimerization activity(GO:0046982)
1.3	4.0	GO:0031720	haptoglobin binding(GO:0031720)
0.1	3.0	GO:0031492	nucleosomal DNA binding(GO:0031492)
0.0	3.0	GO:0051082	unfolded protein binding(GO:0051082)
0.3	2.8	GO:0005344	oxygen transporter activity(GO:0005344)
0.1	2.4	GO:0070888	E-box binding(GO:0070888)
0.1	2.0	GO:0042605	peptide antigen binding(GO:0042605)
0.2	1.9	GO:0008430	selenium binding(GO:0008430)
0.1	1.9	GO:0004861	cyclin-dependent protein serine/threonine kinase inhibitor activity(GO:0004861)
0.1	1.9	GO:0043522	leucine zipper domain binding(GO:0043522)

Showing 1 to 10 of 238 entries

Gene overrepresentation in curated gene sets: canonical pathways category:

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Total log-likelihood	Term	Description
3.2	PID HIF1 TFPATHWAY	HIF-1-alpha transcription factor network
1.5	PID IL3 PATHWAY	IL3-mediated signaling events
1.3	PID P38 MKK3 6PATHWAY	p38 MAPK signaling pathway
1.2	ST WNT BETA CATENIN PATHWAY	Wnt/beta-catenin Pathway
1.1	PID LIS1 PATHWAY	Lissencephaly gene (LIS1) in neuronal migration and development
1.1	PID AURORA A PATHWAY	Aurora A signaling
1.1	PID FRA PATHWAY	Validated transcriptional targets of AP1 family members Fra1 and Fra2
1.1	PID DELTA NP63 PATHWAY	Validated transcriptional targets of deltaNp63 isoforms
0.9	PID PI3K PLC TRK PATHWAY	Trk receptor signaling mediated by PI3K and PLC-gamma
0.7	PID LYMPH ANGIOGENESIS PATHWAY	VEGFR3 signaling in lymphatic endothelium

Showing 1 to 10 of 35 entries

Gene overrepresentation in curated gene sets: REACTOME pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.6	11.6	REACTOME RNA POL I PROMOTER OPENING	Genes involved in RNA Polymerase I Promoter Opening
0.0	3.3	REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE	Genes involved in SRP-dependent cotranslational protein targeting to membrane
0.3	2.8	REACTOME ACTIVATION OF CHAPERONE GENES BY ATF6 ALPHA	Genes involved in Activation of Chaperone Genes by ATF6-alpha
0.0	2.4	REACTOME APC C CDH1 MEDIATED DEGRADATION OF CDC20 AND OTHER APC C CDH1 TARGETED PROTEINS IN LATE MITOSIS EARLY G1	Genes involved in APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1
0.1	2.3	REACTOME CHOLESTEROL BIOSYNTHESIS	Genes involved in Cholesterol biosynthesis
0.0	2.1	REACTOME MITOCHONDRIAL PROTEIN IMPORT	Genes involved in Mitochondrial Protein Import
0.1	1.8	REACTOME POST CHAPERONIN TUBULIN FOLDING PATHWAY	Genes involved in Post-chaperonin tubulin folding pathway
0.1	1.6	REACTOME FACILITATIVE NA INDEPENDENT GLUCOSE TRANSPORTERS	Genes involved in Facilitative Na+-independent glucose transporters
0.1	1.5	REACTOME ROLE OF DCC IN REGULATING APOPTOSIS	Genes involved in Role of DCC in regulating apoptosis
0.1	1.4	REACTOME TETRAHYDROBIOPTERIN BH4 SYNTHESIS RECYCLING SALVAGE AND REGULATION	Genes involved in Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation

Showing 1 to 10 of 73 entries

Results for Ybx1_Nfya_Nfyb_Nfyc_Cebpz

Z-value: 2.65

Motif logo

Transcription factors associated with Ybx1_Nfya_Nfyb_Nfyc_Cebpz

Activity-expression correlation:

Activity profile of Ybx1_Nfya_Nfyb_Nfyc_Cebpz motif

Sorted Z-values of Ybx1_Nfya_Nfyb_Nfyc_Cebpz motif

Top targets:

Network of associatons between targets according to the STRING database.

First level regulatory network of Ybx1_Nfya_Nfyb_Nfyc_Cebpz

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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: