ISMARA results: Crx

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GSE53960: rat RNA-Seq transcriptomic Bodymap

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Results for Crx_Gsc

Z-value: 0.83

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Transcription factors associated with Crx_Gsc

Gene Symbol	Gene ID	Gene Info
Crx NCBI RGD Ensembl	ENSRNOG00000013890	cone-rod homeobox
Gsc NCBI RGD Ensembl	ENSRNOG00000010605	goosecoid homeobox

Activity-expression correlation:

Gene	Promoter	Pearson corr. coef.	P-value	Plot
Crx	rn6_v1_chr1_-_77750960_77750960	0.24	1.1e-05	Click!
Gsc	rn6_v1_chr6_-_128149220_128149220	-0.23	3.4e-05	Click!

Activity profile of Crx_Gsc motif

Sorted Z-values of Crx_Gsc motif

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Promoter	Log-likelihood	Transcript	Gene	Gene Info
chr11_+_57207656 Show fit	31.89	ENSRNOT00000038207 ENSRNOT00000085754	Plcxd2 NCBI RGD Ensembl Show fit	phosphatidylinositol-specific phospholipase C, X domain containing 2
chr1_+_266781617 Show fit	22.58	ENSRNOT00000027417	Ina NCBI RGD Ensembl Show fit	internexin neuronal intermediate filament protein, alpha
chr1_-_266074181 Show fit	21.28	ENSRNOT00000026378	Psd NCBI RGD Ensembl Show fit	pleckstrin and Sec7 domain containing
chr4_+_94696965 Show fit	18.93	ENSRNOT00000064696	Grid2 NCBI RGD Ensembl Show fit	glutamate ionotropic receptor delta type subunit 2
chr8_-_85645718 Show fit	18.63	ENSRNOT00000032185	Gsta2 NCBI RGD Ensembl Show fit	glutathione S-transferase alpha 2
chr19_+_10731855 Show fit	18.60	ENSRNOT00000022277	Pllp NCBI RGD Ensembl Show fit	plasmolipin
chr1_+_100393303 Show fit	18.35	ENSRNOT00000026251	Syt3 NCBI RGD Ensembl Show fit	synaptotagmin 3
chr10_-_27366665 Show fit	18.27	ENSRNOT00000004725	Gabra1 NCBI RGD Ensembl Show fit	gamma-aminobutyric acid type A receptor alpha1 subunit
chr10_-_58693754 Show fit	16.17	ENSRNOT00000071764	Pitpnm3 NCBI RGD Ensembl Show fit	PITPNM family member 3
chr17_+_81455955 Show fit	15.50	ENSRNOT00000044313	Slc39a12 NCBI RGD Ensembl Show fit	solute carrier family 39 member 12

Showing 1 to 10 of 200 entries

Network of associatons between targets according to the STRING database.

First level regulatory network of Crx_Gsc

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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
1.0	31.5	GO:1903861	positive regulation of dendrite extension(GO:1903861)
2.3	22.6	GO:0060052	neurofilament cytoskeleton organization(GO:0060052)
3.5	21.3	GO:0006863	purine nucleobase transport(GO:0006863) nucleobase transport(GO:0015851)
1.4	18.9	GO:0021707	cerebellar granular layer formation(GO:0021684) cerebellar granule cell differentiation(GO:0021707)
2.1	18.6	GO:0001766	membrane raft polarization(GO:0001766) membrane raft distribution(GO:0031580)
1.4	18.6	GO:0042178	xenobiotic catabolic process(GO:0042178)
1.3	18.2	GO:0071420	cellular response to histamine(GO:0071420)
5.8	17.3	GO:1990743	protein sialylation(GO:1990743)
1.4	15.5	GO:0071578	zinc II ion transmembrane import(GO:0071578)
0.5	15.5	GO:0032008	positive regulation of TOR signaling(GO:0032008)

Showing 1 to 10 of 240 entries

Gene overrepresentation in cellular component category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.1	30.9	GO:0030424	axon(GO:0030424)
0.2	30.7	GO:0043197	dendritic spine(GO:0043197)
0.1	27.6	GO:0000139	Golgi membrane(GO:0000139)
0.5	24.2	GO:0098878	ionotropic glutamate receptor complex(GO:0008328) neurotransmitter receptor complex(GO:0098878)
1.4	22.6	GO:0005883	neurofilament(GO:0005883)
0.1	20.5	GO:0043204	perikaryon(GO:0043204)
0.7	18.6	GO:0043218	compact myelin(GO:0043218)
0.1	18.4	GO:0030658	transport vesicle membrane(GO:0030658)
0.0	17.1	GO:0048471	perinuclear region of cytoplasm(GO:0048471)
0.2	16.7	GO:0031225	anchored component of membrane(GO:0031225)

Showing 1 to 10 of 129 entries

Gene overrepresentation in molecular function category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.3	29.3	GO:0008081	phosphoric diester hydrolase activity(GO:0008081)
0.1	25.5	GO:0005525	GTP binding(GO:0005525)
1.8	21.3	GO:0015216	purine nucleotide transmembrane transporter activity(GO:0015216)
0.1	19.6	GO:0005096	GTPase activator activity(GO:0005096)
1.5	18.6	GO:0019911	structural constituent of myelin sheath(GO:0019911)
3.7	18.3	GO:1904315	benzodiazepine receptor activity(GO:0008503) transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential(GO:1904315)
0.9	18.0	GO:0017081	chloride channel regulator activity(GO:0017081)
1.0	17.9	GO:0043295	glutathione binding(GO:0043295)
0.3	17.8	GO:0001786	phosphatidylserine binding(GO:0001786)
0.1	17.7	GO:0005088	Ras guanyl-nucleotide exchange factor activity(GO:0005088)

Showing 1 to 10 of 173 entries

Gene overrepresentation in curated gene sets: canonical pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.3	27.1	PID SMAD2 3NUCLEAR PATHWAY	Regulation of nuclear SMAD2/3 signaling
0.3	14.6	PID RAC1 REG PATHWAY	Regulation of RAC1 activity
0.4	14.5	PID HDAC CLASSII PATHWAY	Signaling events mediated by HDAC Class II
0.4	14.4	ST GA12 PATHWAY	G alpha 12 Pathway
0.4	14.1	PID REELIN PATHWAY	Reelin signaling pathway
0.4	11.7	ST GRANULE CELL SURVIVAL PATHWAY	Granule Cell Survival Pathway is a specific case of more general PAC1 Receptor Pathway.
0.1	10.4	NABA ECM GLYCOPROTEINS	Genes encoding structural ECM glycoproteins
0.4	9.5	PID IL8 CXCR1 PATHWAY	IL8- and CXCR1-mediated signaling events
0.7	9.2	PID P38 GAMMA DELTA PATHWAY	Signaling mediated by p38-gamma and p38-delta
0.1	8.3	PID NOTCH PATHWAY	Notch signaling pathway

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	23.8	REACTOME ACTIVATED NOTCH1 TRANSMITS SIGNAL TO THE NUCLEUS	Genes involved in Activated NOTCH1 Transmits Signal to the Nucleus
0.2	23.5	REACTOME SIGNALING BY RHO GTPASES	Genes involved in Signaling by Rho GTPases
1.2	20.0	REACTOME N GLYCAN ANTENNAE ELONGATION	Genes involved in N-Glycan antennae elongation
0.7	19.9	REACTOME ADHERENS JUNCTIONS INTERACTIONS	Genes involved in Adherens junctions interactions
0.5	18.7	REACTOME GLYCOLYSIS	Genes involved in Glycolysis
0.6	18.6	REACTOME GLUTATHIONE CONJUGATION	Genes involved in Glutathione conjugation
1.1	18.3	REACTOME GABA A RECEPTOR ACTIVATION	Genes involved in GABA A receptor activation
1.0	15.9	REACTOME ACTIVATION OF THE AP1 FAMILY OF TRANSCRIPTION FACTORS	Genes involved in Activation of the AP-1 family of transcription factors
0.4	14.4	REACTOME PHASE II CONJUGATION	Genes involved in Phase II conjugation
0.8	14.1	REACTOME CREB PHOSPHORYLATION THROUGH THE ACTIVATION OF CAMKII	Genes involved in CREB phosphorylation through the activation of CaMKII

Showing 1 to 10 of 72 entries

Results for Crx_Gsc

Z-value: 0.83

Motif logo

Transcription factors associated with Crx_Gsc

Activity-expression correlation:

Activity profile of Crx_Gsc motif

Sorted Z-values of Crx_Gsc motif

Top targets:

Network of associatons between targets according to the STRING database.

First level regulatory network of Crx_Gsc

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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: