ISMARA results: Rxra

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GSE53960: rat RNA-Seq transcriptomic Bodymap

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Results for Rxra

Z-value: 0.99

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Transcription factors associated with Rxra

Gene Symbol	Gene ID	Gene Info
Rxra NCBI RGD Ensembl	ENSRNOG00000009446	retinoid X receptor alpha

Activity-expression correlation:

Gene	Promoter	Pearson corr. coef.	P-value	Plot
Rxra	rn6_v1_chr3_+_6211789_6211789	-0.39	9.4e-13	Click!

Activity profile of Rxra motif

Sorted Z-values of Rxra motif

Top targets:

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Promoter	Log-likelihood	Transcript	Gene	Gene Info
chr3_+_113318563 Show fit	42.02	ENSRNOT00000089230	Ckmt1 NCBI RGD Ensembl Show fit	creatine kinase, mitochondrial 1
chr9_-_92530938 Show fit	28.10	ENSRNOT00000064875	Slc16a14 NCBI RGD Ensembl Show fit	solute carrier family 16, member 14
chr2_-_225107283 Show fit	27.95	ENSRNOT00000055711	Slc44a3 NCBI RGD Ensembl Show fit	solute carrier family 44, member 3
chr17_+_23661429 Show fit	26.49	ENSRNOT00000046523	Phactr1 NCBI RGD Ensembl Show fit	phosphatase and actin regulator 1
chr4_-_176294997 Show fit	24.58	ENSRNOT00000015112 ENSRNOT00000051461 ENSRNOT00000000026 ENSRNOT00000039877 ENSRNOT00000049303	Slc21a4 NCBI RGD Ensembl Show fit	kidney specific organic anion transporter
chr10_-_65692016 Show fit	24.33	ENSRNOT00000085074 ENSRNOT00000038690	Slc13a2 NCBI RGD Ensembl Show fit	solute carrier family 13 member 2
chr18_-_1946840 Show fit	23.20	ENSRNOT00000041878	Abhd3 NCBI RGD Ensembl Show fit	abhydrolase domain containing 3
chr1_-_31122093 Show fit	23.13	ENSRNOT00000016712	NEWGENE_1307525 NCBI RGD Ensembl Show fit	SOGA family member 3
chrX_+_14019961 Show fit	22.93	ENSRNOT00000004785	Sytl5 NCBI RGD Ensembl Show fit	synaptotagmin-like 5
chr7_+_139685573 Show fit	22.92	ENSRNOT00000088376	Pfkm NCBI RGD Ensembl Show fit	phosphofructokinase, muscle

Showing 1 to 10 of 200 entries

Network of associatons between targets according to the STRING database.

First level regulatory network of Rxra

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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
0.4	42.0	GO:0032091	negative regulation of protein binding(GO:0032091)
0.1	27.7	GO:0006814	sodium ion transport(GO:0006814)
0.5	26.7	GO:0048791	calcium ion-regulated exocytosis of neurotransmitter(GO:0048791)
0.3	26.5	GO:0043149	contractile actin filament bundle assembly(GO:0030038) stress fiber assembly(GO:0043149)
6.1	24.6	GO:0051958	methotrexate transport(GO:0051958)
0.0	23.3	GO:0050911	detection of chemical stimulus involved in sensory perception of smell(GO:0050911)
0.6	23.2	GO:0046470	phosphatidylcholine metabolic process(GO:0046470)
5.7	22.9	GO:0061622	glycolytic process through glucose-1-phosphate(GO:0061622)
3.6	21.5	GO:1900272	negative regulation of long-term synaptic potentiation(GO:1900272)
6.7	20.0	GO:0033512	L-lysine catabolic process to acetyl-CoA via saccharopine(GO:0033512)

Showing 1 to 10 of 131 entries

Gene overrepresentation in cellular component category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.3	57.0	GO:0043204	perikaryon(GO:0043204)
0.0	43.3	GO:0005739	mitochondrion(GO:0005739)
0.1	36.7	GO:0030425	dendrite(GO:0030425)
0.1	29.1	GO:0070382	exocytic vesicle(GO:0070382)
7.6	22.9	GO:0005945	6-phosphofructokinase complex(GO:0005945)
0.1	22.9	GO:0016324	apical plasma membrane(GO:0016324)
5.4	21.5	GO:1990761	growth cone lamellipodium(GO:1990761)
0.4	20.3	GO:0030964	mitochondrial respiratory chain complex I(GO:0005747) NADH dehydrogenase complex(GO:0030964) respiratory chain complex I(GO:0045271)
0.9	18.6	GO:0001518	voltage-gated sodium channel complex(GO:0001518)
0.1	17.0	GO:0045202	synapse(GO:0045202)

Showing 1 to 10 of 69 entries

Gene overrepresentation in molecular function category:

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Log-likelihood per target	Total log-likelihood	Term	Description
1.8	47.9	GO:0008157	protein phosphatase 1 binding(GO:0008157)
6.0	42.0	GO:0004111	creatine kinase activity(GO:0004111)
0.4	33.2	GO:0030276	clathrin binding(GO:0030276)
6.1	24.6	GO:0015350	methotrexate transporter activity(GO:0015350)
3.9	23.2	GO:0008970	phosphatidylcholine 1-acylhydrolase activity(GO:0008970)
5.7	22.9	GO:0003872	6-phosphofructokinase activity(GO:0003872)
1.7	20.4	GO:0004499	N,N-dimethylaniline monooxygenase activity(GO:0004499)
5.0	20.0	GO:0016212	kynurenine-oxoglutarate transaminase activity(GO:0016212) kynurenine aminotransferase activity(GO:0036137)
1.5	19.9	GO:0030215	semaphorin receptor binding(GO:0030215)
5.0	19.8	GO:0060072	large conductance calcium-activated potassium channel activity(GO:0060072)

Showing 1 to 10 of 113 entries

Gene overrepresentation in curated gene sets: canonical pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.5	19.8	PID HIF2PATHWAY	HIF-2-alpha transcription factor network
0.2	17.2	PID MYC ACTIV PATHWAY	Validated targets of C-MYC transcriptional activation
0.1	16.4	NABA ECM GLYCOPROTEINS	Genes encoding structural ECM glycoproteins
0.4	15.0	PID EPHA FWDPATHWAY	EPHA forward signaling
0.1	13.1	WNT SIGNALING	Genes related to Wnt-mediated signal transduction
0.3	10.5	PID NCADHERIN PATHWAY	N-cadherin signaling events
0.1	8.8	NABA ECM AFFILIATED	Genes encoding proteins affiliated structurally or functionally to extracellular matrix proteins
0.2	7.4	PID RXR VDR PATHWAY	RXR and RAR heterodimerization with other nuclear receptor
0.2	6.1	SA B CELL RECEPTOR COMPLEXES	Antigen binding to B cell receptors activates protein tyrosine kinases, such as the Src family, which ultimate activate MAP kinases.
0.1	6.1	PID P73PATHWAY	p73 transcription factor network

Showing 1 to 10 of 19 entries

Gene overrepresentation in curated gene sets: REACTOME pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
1.1	27.9	REACTOME SYNTHESIS OF PC	Genes involved in Synthesis of PC
0.7	27.2	REACTOME GLYCOLYSIS	Genes involved in Glycolysis
1.7	24.3	REACTOME BILE SALT AND ORGANIC ANION SLC TRANSPORTERS	Genes involved in Bile salt and organic anion SLC transporters
2.3	21.0	REACTOME ABACAVIR TRANSPORT AND METABOLISM	Genes involved in Abacavir transport and metabolism
2.2	20.0	REACTOME TRYPTOPHAN CATABOLISM	Genes involved in Tryptophan catabolism
0.2	16.4	REACTOME NUCLEAR RECEPTOR TRANSCRIPTION PATHWAY	Genes involved in Nuclear Receptor transcription pathway
0.3	15.6	REACTOME VOLTAGE GATED POTASSIUM CHANNELS	Genes involved in Voltage gated Potassium channels
0.2	15.1	REACTOME MHC CLASS II ANTIGEN PRESENTATION	Genes involved in MHC class II antigen presentation
0.2	15.0	REACTOME RESPIRATORY ELECTRON TRANSPORT ATP SYNTHESIS BY CHEMIOSMOTIC COUPLING AND HEAT PRODUCTION BY UNCOUPLING PROTEINS	Genes involved in Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.
0.3	13.3	REACTOME MITOCHONDRIAL PROTEIN IMPORT	Genes involved in Mitochondrial Protein Import

Showing 1 to 10 of 41 entries

Results for Rxra

Z-value: 0.99

Motif logo

Transcription factors associated with Rxra

Activity-expression correlation:

Activity profile of Rxra motif

Sorted Z-values of Rxra motif

Top targets:

Network of associatons between targets according to the STRING database.

First level regulatory network of Rxra

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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: