ISMARA results: Hoxb8

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GSE53960: rat RNA-Seq transcriptomic Bodymap

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Results for Hoxb8_Pdx1

Z-value: 1.06

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Transcription factors associated with Hoxb8_Pdx1

Gene Symbol	Gene ID	Gene Info
Hoxb8 NCBI RGD Ensembl	ENSRNOG00000007585	homeo box B8
Pdx1 NCBI RGD Ensembl	ENSRNOG00000046458	pancreatic and duodenal homeobox 1

Activity-expression correlation:

Gene	Promoter	Pearson corr. coef.	P-value	Plot
Hoxb8	rn6_v1_chr10_+_84131495_84131495	0.33	1.5e-09	Click!
Pdx1	rn6_v1_chr12_-_9501213_9501213	0.11	5.4e-02	Click!

Activity profile of Hoxb8_Pdx1 motif

Sorted Z-values of Hoxb8_Pdx1 motif

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Promoter	Log-likelihood	Transcript	Gene	Gene Info
chr1_+_201620642 Show fit	64.51	ENSRNOT00000093674	Dmbt1 NCBI RGD Ensembl Show fit	deleted in malignant brain tumors 1
chr2_-_105089659 Show fit	56.60	ENSRNOT00000043381	Cpb1 NCBI RGD Ensembl Show fit	carboxypeptidase B1
chr7_+_125288081 Show fit	54.49	ENSRNOT00000085216	Parvg NCBI RGD Ensembl Show fit	parvin, gamma
chr16_-_29936307 Show fit	44.44	ENSRNOT00000088707	Ddx60 NCBI RGD Ensembl Show fit	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60
chr3_-_23020441 Show fit	38.09	ENSRNOT00000017651	Nr5a1 NCBI RGD Ensembl Show fit	nuclear receptor subfamily 5, group A, member 1
chr1_-_197821936 Show fit	33.68	ENSRNOT00000055027	Cd19 NCBI RGD Ensembl Show fit	CD19 molecule
chr10_+_84200880 Show fit	29.37	ENSRNOT00000011213	Hoxb2 NCBI RGD Ensembl Show fit	homeobox B2
chr16_-_31301880 Show fit	25.24	ENSRNOT00000084847 ENSRNOT00000083943	AABR07025272.1 NCBI RGD Ensembl Show fit
chr16_-_71040847 Show fit	25.16	ENSRNOT00000020606	Star NCBI RGD Ensembl Show fit	steroidogenic acute regulatory protein
chr4_-_82133605 Show fit	23.49	ENSRNOT00000008023	NEWGENE_2813 NCBI RGD Ensembl Show fit	homeobox A2

Showing 1 to 10 of 200 entries

Network of associatons between targets according to the STRING database.

First level regulatory network of Hoxb8_Pdx1

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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
3.6	71.7	GO:0001833	inner cell mass cell proliferation(GO:0001833)
0.6	58.1	GO:0031532	actin cytoskeleton reorganization(GO:0031532)
9.5	38.1	GO:2000195	negative regulation of female gonad development(GO:2000195)
2.5	35.6	GO:0006968	cellular defense response(GO:0006968)
5.9	35.1	GO:0034757	negative regulation of iron ion transport(GO:0034757)
9.8	29.4	GO:0021569	rhombomere 3 development(GO:0021569) rhombomere 4 development(GO:0021570)
8.4	25.2	GO:0017143	insecticide metabolic process(GO:0017143)
2.0	21.7	GO:2000271	positive regulation of fibroblast apoptotic process(GO:2000271)
0.4	15.4	GO:0000462	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)(GO:0000462)
3.8	15.2	GO:1903225	negative regulation of endodermal cell differentiation(GO:1903225)

Showing 1 to 10 of 184 entries

Gene overrepresentation in cellular component category:

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Log-likelihood per target	Total log-likelihood	Term	Description
3.4	64.5	GO:0042589	zymogen granule membrane(GO:0042589)
0.3	37.1	GO:0090575	RNA polymerase II transcription factor complex(GO:0090575)
0.0	33.5	GO:0005654	nucleoplasm(GO:0005654)
0.1	27.2	GO:0009897	external side of plasma membrane(GO:0009897)
0.1	25.7	GO:0016607	nuclear speck(GO:0016607)
1.3	21.6	GO:0030061	mitochondrial crista(GO:0030061)
0.7	20.9	GO:0034364	high-density lipoprotein particle(GO:0034364)
3.9	19.3	GO:0031262	Ndc80 complex(GO:0031262)
0.2	16.7	GO:0022627	cytosolic small ribosomal subunit(GO:0022627)
0.4	16.3	GO:0046658	anchored component of plasma membrane(GO:0046658)

Showing 1 to 10 of 93 entries

Gene overrepresentation in molecular function category:

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Log-likelihood per target	Total log-likelihood	Term	Description
2.4	64.6	GO:0004181	metallocarboxypeptidase activity(GO:0004181)
9.1	63.9	GO:0035375	zymogen binding(GO:0035375)
0.4	39.1	GO:0000980	RNA polymerase II distal enhancer sequence-specific DNA binding(GO:0000980)
0.1	36.2	GO:0001071	nucleic acid binding transcription factor activity(GO:0001071) transcription factor activity, sequence-specific DNA binding(GO:0003700)
10.4	31.2	GO:0004769	steroid delta-isomerase activity(GO:0004769)
0.2	30.1	GO:0005057	receptor signaling protein activity(GO:0005057)
0.1	30.0	GO:0003735	structural constituent of ribosome(GO:0003735)
0.3	26.5	GO:0003823	antigen binding(GO:0003823)
1.1	25.2	GO:0017127	cholesterol transporter activity(GO:0017127)
0.1	19.7	GO:0001077	transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding(GO:0001077)

Showing 1 to 10 of 147 entries

Gene overrepresentation in curated gene sets: canonical pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
1.0	57.3	PID ILK PATHWAY	Integrin-linked kinase signaling
0.2	48.2	NABA ECM GLYCOPROTEINS	Genes encoding structural ECM glycoproteins
0.8	34.6	SIG PIP3 SIGNALING IN B LYMPHOCYTES	Genes related to PIP3 signaling in B lymphocytes
0.1	31.3	NABA ECM REGULATORS	Genes encoding enzymes and their regulators involved in the remodeling of the extracellular matrix
0.5	25.4	NABA COLLAGENS	Genes encoding collagen proteins
0.7	24.7	PID P38 ALPHA BETA PATHWAY	Regulation of p38-alpha and p38-beta
0.8	19.8	PID EPHA2 FWD PATHWAY	EPHA2 forward signaling
0.1	12.5	PID P53 DOWNSTREAM PATHWAY	Direct p53 effectors
0.3	11.7	PID ERBB4 PATHWAY	ErbB4 signaling events
0.2	11.5	PID IL4 2PATHWAY	IL4-mediated signaling events

Showing 1 to 10 of 37 entries

Gene overrepresentation in curated gene sets: REACTOME pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.8	32.3	REACTOME ANTIGEN ACTIVATES B CELL RECEPTOR LEADING TO GENERATION OF SECOND MESSENGERS	Genes involved in Antigen Activates B Cell Receptor Leading to Generation of Second Messengers
2.6	31.2	REACTOME ANDROGEN BIOSYNTHESIS	Genes involved in Androgen biosynthesis
0.4	27.1	REACTOME NUCLEAR RECEPTOR TRANSCRIPTION PATHWAY	Genes involved in Nuclear Receptor transcription pathway
0.3	26.8	REACTOME MITOTIC PROMETAPHASE	Genes involved in Mitotic Prometaphase
1.2	25.2	REACTOME STEROID HORMONES	Genes involved in Steroid hormones
0.2	16.1	REACTOME CELL SURFACE INTERACTIONS AT THE VASCULAR WALL	Genes involved in Cell surface interactions at the vascular wall
0.7	15.5	REACTOME GENERATION OF SECOND MESSENGER MOLECULES	Genes involved in Generation of second messenger molecules
0.6	13.2	REACTOME N GLYCAN ANTENNAE ELONGATION IN THE MEDIAL TRANS GOLGI	Genes involved in N-glycan antennae elongation in the medial/trans-Golgi
0.7	12.5	REACTOME CHYLOMICRON MEDIATED LIPID TRANSPORT	Genes involved in Chylomicron-mediated lipid transport
0.6	11.7	REACTOME PROLACTIN RECEPTOR SIGNALING	Genes involved in Prolactin receptor signaling

Showing 1 to 10 of 74 entries

Results for Hoxb8_Pdx1

Z-value: 1.06

Motif logo

Transcription factors associated with Hoxb8_Pdx1

Activity-expression correlation:

Activity profile of Hoxb8_Pdx1 motif

Sorted Z-values of Hoxb8_Pdx1 motif

Top targets:

Network of associatons between targets according to the STRING database.

First level regulatory network of Hoxb8_Pdx1

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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: