ISMARA results: RARA

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GNF SymAtlas + NCI-60 cancer cell lines, comparison of cancers vs non-cancers, human (Su, 2004; Ross, 2000)

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Results for RARA

Z-value: 0.15

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Transcription factors associated with RARA

Gene Symbol	Gene ID	Gene Info
RARA Ensembl NCBI GeneCards UniProt NextProt	ENSG00000131759.13	retinoic acid receptor alpha

Activity-expression correlation:

Gene	Promoter	Pearson corr. coef.	P-value	Plot
RARA	hg19_v2_chr17_+_38474489_38474548	-0.04	6.0e-01	Click!

Activity profile of RARA motif

Sorted Z-values of RARA motif

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Promoter	Log-likelihood	Transcript	Gene	Gene Info
chr12_+_54378923 Show fit	8.48	ENST00000303460.4	HOXC10 Ensembl NCBI GeneCards UniProt NextProt Show fit	homeobox C10
chr4_+_107236692 Show fit	7.31	ENST00000510207.1	AIMP1 Ensembl NCBI GeneCards UniProt NextProt Show fit	aminoacyl tRNA synthetase complex-interacting multifunctional protein 1
chr13_+_43597269 Show fit	7.21	ENST00000379221.2	DNAJC15 Ensembl NCBI GeneCards UniProt NextProt Show fit	DnaJ (Hsp40) homolog, subfamily C, member 15
chr16_-_11680791 Show fit	6.37	ENST00000571976.1 ENST00000413364.2	LITAF Ensembl NCBI GeneCards UniProt NextProt Show fit	lipopolysaccharide-induced TNF factor
chr10_+_17270214 Show fit	6.16	ENST00000544301.1	VIM Ensembl NCBI GeneCards UniProt NextProt Show fit	vimentin
chr10_+_115438920 Show fit	5.72	ENST00000429617.1 ENST00000369331.4	CASP7 Ensembl NCBI GeneCards UniProt NextProt Show fit	caspase 7, apoptosis-related cysteine peptidase
chr5_+_65440032 Show fit	5.47	ENST00000334121.6	SREK1 Ensembl NCBI GeneCards UniProt NextProt Show fit	splicing regulatory glutamine/lysine-rich protein 1
chr1_-_53704157 Show fit	4.71	ENST00000371466.4 ENST00000371470.3	MAGOH Ensembl NCBI GeneCards UniProt NextProt Show fit	mago-nashi homolog, proliferation-associated (Drosophila)
chr16_-_11680759 Show fit	4.64	ENST00000571459.1 ENST00000570798.1 ENST00000572255.1 ENST00000574763.1 ENST00000574703.1 ENST00000571277.1 ENST00000381810.3	LITAF Ensembl NCBI GeneCards UniProt NextProt Show fit	lipopolysaccharide-induced TNF factor
chr4_+_107236847 Show fit	4.52	ENST00000358008.3	AIMP1 Ensembl NCBI GeneCards UniProt NextProt Show fit	aminoacyl tRNA synthetase complex-interacting multifunctional protein 1

Showing 1 to 10 of 200 entries

Network of associatons between targets according to the STRING database.

First level regulatory network of RARA

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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	18.3	GO:0001937	negative regulation of endothelial cell proliferation(GO:0001937)
1.2	13.5	GO:0035986	senescence-associated heterochromatin focus assembly(GO:0035986)
0.2	10.6	GO:0000381	regulation of alternative mRNA splicing, via spliceosome(GO:0000381)
0.3	9.8	GO:0042347	negative regulation of NF-kappaB import into nucleus(GO:0042347)
0.9	8.5	GO:0021520	spinal cord motor neuron cell fate specification(GO:0021520)
0.7	8.1	GO:0038203	TORC2 signaling(GO:0038203)
0.2	7.6	GO:0090503	RNA phosphodiester bond hydrolysis, exonucleolytic(GO:0090503)
0.7	6.6	GO:0010265	SCF complex assembly(GO:0010265)
0.6	6.2	GO:0060020	Bergmann glial cell differentiation(GO:0060020)
0.7	5.7	GO:0072733	response to staurosporine(GO:0072733) cellular response to staurosporine(GO:0072734)

Showing 1 to 10 of 208 entries

Gene overrepresentation in cellular_component category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.1	16.7	GO:0005681	spliceosomal complex(GO:0005681)
3.3	16.3	GO:0017102	methionyl glutamyl tRNA synthetase complex(GO:0017102)
1.2	13.5	GO:0035985	senescence-associated heterochromatin focus(GO:0035985)
1.8	11.0	GO:0098560	cytoplasmic side of late endosome membrane(GO:0098560)
0.1	9.6	GO:0005758	mitochondrial intermembrane space(GO:0005758)
0.9	8.5	GO:0019907	cyclin-dependent protein kinase activating kinase holoenzyme complex(GO:0019907)
0.5	8.1	GO:0031932	TORC2 complex(GO:0031932)
0.0	7.1	GO:0005884	actin filament(GO:0005884)
0.4	6.6	GO:0030285	integral component of synaptic vesicle membrane(GO:0030285) intrinsic component of synaptic vesicle membrane(GO:0098563)
0.6	5.6	GO:0071541	eukaryotic translation initiation factor 3 complex, eIF3m(GO:0071541)

Showing 1 to 10 of 114 entries

Gene overrepresentation in molecular_function category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.4	19.9	GO:0000049	tRNA binding(GO:0000049)
0.3	12.9	GO:0050699	WW domain binding(GO:0050699)
0.0	12.5	GO:0001228	transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding(GO:0001228)
0.6	10.7	GO:0004861	cyclin-dependent protein serine/threonine kinase inhibitor activity(GO:0004861)
0.2	8.9	GO:0016896	exoribonuclease activity, producing 5'-phosphomonoesters(GO:0016896)
0.0	8.1	GO:0031625	ubiquitin protein ligase binding(GO:0031625)
0.2	6.9	GO:0070717	poly-purine tract binding(GO:0070717)
0.1	6.6	GO:0042974	retinoic acid receptor binding(GO:0042974)
1.0	6.2	GO:1990254	keratin filament binding(GO:1990254)
0.2	5.7	GO:0097200	cysteine-type endopeptidase activity involved in execution phase of apoptosis(GO:0097200)

Showing 1 to 10 of 166 entries

Gene overrepresentation in C2:CP category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.5	12.6	SA REG CASCADE OF CYCLIN EXPR	Expression of cyclins regulates progression through the cell cycle by activating cyclin-dependent kinases.
0.1	12.0	PID MTOR 4PATHWAY	mTOR signaling pathway
0.1	11.7	NABA ECM GLYCOPROTEINS	Genes encoding structural ECM glycoproteins
0.2	7.9	PID WNT NONCANONICAL PATHWAY	Noncanonical Wnt signaling pathway
0.1	7.7	PID DELTA NP63 PATHWAY	Validated transcriptional targets of deltaNp63 isoforms
0.1	7.0	PID FOXM1 PATHWAY	FOXM1 transcription factor network
0.2	5.7	SA CASPASE CASCADE	Apoptosis is mediated by caspases, cysteine proteases arranged in a proteolytic cascade.
0.1	5.7	PID IL1 PATHWAY	IL1-mediated signaling events
0.0	5.6	PID P53 DOWNSTREAM PATHWAY	Direct p53 effectors
0.2	5.4	PID BETA CATENIN DEG PATHWAY	Degradation of beta catenin

Showing 1 to 10 of 39 entries

Gene overrepresentation in C2:CP:REACTOME category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.3	18.0	REACTOME G1 PHASE	Genes involved in G1 Phase
0.5	16.3	REACTOME CYTOSOLIC TRNA AMINOACYLATION	Genes involved in Cytosolic tRNA aminoacylation
0.4	12.4	REACTOME CASPASE MEDIATED CLEAVAGE OF CYTOSKELETAL PROTEINS	Genes involved in Caspase-mediated cleavage of cytoskeletal proteins
0.1	9.4	REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM	Genes involved in Transport of Mature Transcript to Cytoplasm
0.4	8.4	REACTOME G2 M DNA DAMAGE CHECKPOINT	Genes involved in G2/M DNA damage checkpoint
0.0	6.7	REACTOME TRANSLATION	Genes involved in Translation
0.2	6.2	REACTOME LIPOPROTEIN METABOLISM	Genes involved in Lipoprotein metabolism
0.3	4.9	REACTOME PECAM1 INTERACTIONS	Genes involved in PECAM1 interactions
0.0	4.9	REACTOME CLASS B 2 SECRETIN FAMILY RECEPTORS	Genes involved in Class B/2 (Secretin family receptors)
0.1	4.3	REACTOME RNA POL I RNA POL III AND MITOCHONDRIAL TRANSCRIPTION	Genes involved in RNA Polymerase I, RNA Polymerase III, and Mitochondrial Transcription

Showing 1 to 10 of 73 entries

Results for RARA

Z-value: 0.15

Motif logo

Transcription factors associated with RARA

Activity-expression correlation:

Activity profile of RARA motif

Sorted Z-values of RARA motif

Top targets:

Network of associatons between targets according to the STRING database.

First level regulatory network of RARA

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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 C2:CP category:

Gene overrepresentation in C2:CP:REACTOME category: