ISMARA results: Ybx1_Nfya_Nfyb_Nfyc

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GSE53960: rat RNA-Seq transcriptomic Bodymap

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Results for Ybx1_Nfya_Nfyb_Nfyc_Cebpz

Z-value: 4.86

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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
Nfya	rn6_v1_chr9_+_14551758_14551758	0.49	7.6e-21	Click!
Cebpz	rn6_v1_chr6_-_1534488_1534488	0.39	6.9e-13	Click!
Nfyc	rn6_v1_chr5_-_139748489_139748489	0.22	9.1e-05	Click!
Nfyb	rn6_v1_chr7_+_27089278_27089278	0.22	1.0e-04	Click!
Ybx1	rn6_v1_chr5_-_138336475_138336475	0.15	5.7e-03	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
chr17_+_43423111 Show fit	272.02	ENSRNOT00000022630	Hist1h2ba NCBI RGD Ensembl Show fit	histone cluster 1 H2B family member a
chr17_-_43422846 Show fit	258.55	ENSRNOT00000050526	Hist1h2aa NCBI RGD Ensembl Show fit	histone cluster 1 H2A family member a
chr4_+_157348020 Show fit	249.01	ENSRNOT00000020803	Cdca3 NCBI RGD Ensembl Show fit	cell division cycle associated 3
chr2_-_112831476 Show fit	240.97	ENSRNOT00000018055	Ect2 NCBI RGD Ensembl Show fit	epithelial cell transforming 2
chr19_+_25077918 Show fit	218.77	ENSRNOT00000006964	Asf1b NCBI RGD Ensembl Show fit	anti-silencing function 1B histone chaperone
chr10_-_74413745 Show fit	198.03	ENSRNOT00000038296	Prr11 NCBI RGD Ensembl Show fit	proline rich 11
chr10_-_86932154 Show fit	187.53	ENSRNOT00000085344	Top2a NCBI RGD Ensembl Show fit	topoisomerase (DNA) II alpha
chr13_+_56546021 Show fit	186.28	ENSRNOT00000016797	Aspm NCBI RGD Ensembl Show fit	abnormal spindle microtubule assembly
chr16_-_36080191 Show fit	181.93	ENSRNOT00000017635	Hmgb2l1 NCBI RGD Ensembl Show fit	high mobility group box 2-like 1
chr8_+_48665652 Show fit	156.21	ENSRNOT00000059715	H2afx NCBI RGD Ensembl Show fit	H2A histone family, member X

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
16.6	1559.9	GO:0006342	chromatin silencing(GO:0006342)
16.0	1087.4	GO:0006334	nucleosome assembly(GO:0006334)
27.6	745.8	GO:0006335	DNA replication-dependent nucleosome assembly(GO:0006335) DNA replication-dependent nucleosome organization(GO:0034723)
10.9	492.5	GO:0051310	metaphase plate congression(GO:0051310)
7.0	392.9	GO:0000070	mitotic sister chromatid segregation(GO:0000070)
25.9	362.0	GO:0051988	regulation of attachment of spindle microtubules to kinetochore(GO:0051988)
2.5	290.7	GO:0007059	chromosome segregation(GO:0007059)
45.3	272.0	GO:0035093	spermatogenesis, exchange of chromosomal proteins(GO:0035093)
18.4	239.8	GO:0007076	mitotic chromosome condensation(GO:0007076)
77.6	232.9	GO:1902103	metaphase/anaphase transition of meiotic cell cycle(GO:0044785) regulation of metaphase/anaphase transition of meiotic cell cycle(GO:1902102) negative regulation of metaphase/anaphase transition of meiotic cell cycle(GO:1902103) regulation of meiotic chromosome separation(GO:1905132) negative regulation of meiotic chromosome separation(GO:1905133)

Showing 1 to 10 of 533 entries

Gene overrepresentation in cellular component category:

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Log-likelihood per target	Total log-likelihood	Term	Description
37.3	3654.8	GO:0000786	nucleosome(GO:0000786)
7.0	674.3	GO:0000776	kinetochore(GO:0000776)
2.8	405.4	GO:0044450	microtubule organizing center part(GO:0044450)
1.7	381.3	GO:0000790	nuclear chromatin(GO:0000790)
79.4	317.8	GO:0097149	centralspindlin complex(GO:0097149)
7.1	262.4	GO:0005876	spindle microtubule(GO:0005876)
2.2	251.6	GO:0005913	cell-cell adherens junction(GO:0005913)
2.9	247.1	GO:0000793	condensed chromosome(GO:0000793)
12.6	238.8	GO:0010369	chromocenter(GO:0010369)
28.9	231.5	GO:0000235	astral microtubule(GO:0000235) aster(GO:0005818)

Showing 1 to 10 of 236 entries

Gene overrepresentation in molecular function category:

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Log-likelihood per target	Total log-likelihood	Term	Description
3.2	1898.4	GO:0046982	protein heterodimerization activity(GO:0046982)
7.5	1424.3	GO:0042393	histone binding(GO:0042393)
1.4	472.0	GO:0003682	chromatin binding(GO:0003682)
5.6	389.3	GO:0003777	microtubule motor activity(GO:0003777)
0.9	345.8	GO:0004842	ubiquitin-protein transferase activity(GO:0004842)
3.1	312.9	GO:0017048	Rho GTPase binding(GO:0017048)
30.8	277.1	GO:0043515	kinetochore binding(GO:0043515)
4.8	261.4	GO:0031490	chromatin DNA binding(GO:0031490)
64.0	255.9	GO:0061575	cyclin-dependent protein serine/threonine kinase activator activity(GO:0061575)
0.3	247.7	GO:0003677	DNA binding(GO:0003677)

Showing 1 to 10 of 324 entries

Gene overrepresentation in curated gene sets: canonical pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
25.0	1223.1	PID FOXM1 PATHWAY	FOXM1 transcription factor network
16.5	842.3	PID PLK1 PATHWAY	PLK1 signaling events
8.3	415.9	PID FANCONI PATHWAY	Fanconi anemia pathway
7.0	245.8	PID AURORA B PATHWAY	Aurora B signaling
3.7	219.3	PID DELTA NP63 PATHWAY	Validated transcriptional targets of deltaNp63 isoforms
3.5	183.7	PID E2F PATHWAY	E2F transcription factor network
6.9	138.3	PID SMAD2 3PATHWAY	Regulation of cytoplasmic and nuclear SMAD2/3 signaling
1.2	121.7	PID P53 DOWNSTREAM PATHWAY	Direct p53 effectors
8.1	105.8	PID RANBP2 PATHWAY	Sumoylation by RanBP2 regulates transcriptional repression
2.0	95.3	PID TELOMERASE PATHWAY	Regulation of Telomerase

Showing 1 to 10 of 76 entries

Gene overrepresentation in curated gene sets: REACTOME pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
54.3	1410.6	REACTOME RNA POL I PROMOTER OPENING	Genes involved in RNA Polymerase I Promoter Opening
7.7	591.0	REACTOME MITOTIC PROMETAPHASE	Genes involved in Mitotic Prometaphase
25.7	410.7	REACTOME CYCLIN A B1 ASSOCIATED EVENTS DURING G2 M TRANSITION	Genes involved in Cyclin A/B1 associated events during G2/M transition
16.7	399.8	REACTOME DEPOSITION OF NEW CENPA CONTAINING NUCLEOSOMES AT THE CENTROMERE	Genes involved in Deposition of New CENPA-containing Nucleosomes at the Centromere
12.0	372.8	REACTOME KINESINS	Genes involved in Kinesins
13.9	319.8	REACTOME APC CDC20 MEDIATED DEGRADATION OF NEK2A	Genes involved in APC-Cdc20 mediated degradation of Nek2A
4.3	270.4	REACTOME NRAGE SIGNALS DEATH THROUGH JNK	Genes involved in NRAGE signals death through JNK
23.9	262.7	REACTOME APOPTOSIS INDUCED DNA FRAGMENTATION	Genes involved in Apoptosis induced DNA fragmentation
2.4	234.2	REACTOME MRNA SPLICING	Genes involved in mRNA Splicing
16.5	181.1	REACTOME UNWINDING OF DNA	Genes involved in Unwinding of DNA

Showing 1 to 10 of 115 entries

Results for Ybx1_Nfya_Nfyb_Nfyc_Cebpz

Z-value: 4.86

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: