ISMARA results: Lhx5_Lmx1b

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GSE53960: rat RNA-Seq transcriptomic Bodymap

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Results for Lhx5_Lmx1b_Lhx1

Z-value: 0.85

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Transcription factors associated with Lhx5_Lmx1b_Lhx1

Gene Symbol	Gene ID	Gene Info
Lhx5 NCBI RGD Ensembl	ENSRNOG00000001392	LIM homeobox 5
Lmx1b NCBI RGD Ensembl	ENSRNOG00000017019	LIM homeobox transcription factor 1 beta
Lhx1 NCBI RGD Ensembl	ENSRNOG00000002812	LIM homeobox 1

Activity-expression correlation:

Gene	Promoter	Pearson corr. coef.	P-value	Plot
Lhx1	rn6_v1_chr10_-_71849293_71849293	-0.51	6.6e-23	Click!
Lhx5	rn6_v1_chr12_-_41671437_41671437	-0.46	2.3e-18	Click!
Lmx1b	rn6_v1_chr3_-_12686869_12686869	-0.20	2.3e-04	Click!

Activity profile of Lhx5_Lmx1b_Lhx1 motif

Sorted Z-values of Lhx5_Lmx1b_Lhx1 motif

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Promoter	Log-likelihood	Transcript	Gene	Gene Info
chr10_+_54352270 Show fit	46.38	ENSRNOT00000036752	Dhrs7c NCBI RGD Ensembl Show fit	dehydrogenase/reductase 7C
chr4_+_29535852 Show fit	41.84	ENSRNOT00000087619	NEWGENE_621351 NCBI RGD Ensembl Show fit	collagen, type I, alpha 2
chrX_-_40086870 Show fit	38.01	ENSRNOT00000010027	Smpx NCBI RGD Ensembl Show fit	small muscle protein, X-linked
chr4_-_41212072 Show fit	30.54	ENSRNOT00000085596	Ppp1r3a NCBI RGD Ensembl Show fit	protein phosphatase 1, regulatory subunit 3A
chr4_+_180291389 Show fit	29.17	ENSRNOT00000002465	Sspn NCBI RGD Ensembl Show fit	sarcospan
chr3_-_37854561 Show fit	27.77	ENSRNOT00000076095	Neb NCBI RGD Ensembl Show fit	nebulin
chr17_+_25082056 Show fit	26.52	ENSRNOT00000037041	AABR07027339.1 NCBI RGD Ensembl Show fit
chr13_-_90074952 Show fit	24.18	ENSRNOT00000038006	Slamf7 NCBI RGD Ensembl Show fit	SLAM family member 7
chr4_+_163349125 Show fit	23.46	ENSRNOT00000084823	Klre1 NCBI RGD Ensembl Show fit	killer cell lectin-like receptor, family E, member 1
chr5_+_165724027 Show fit	20.87	ENSRNOT00000018000	Casz1 NCBI RGD Ensembl Show fit	castor zinc finger 1

Showing 1 to 10 of 200 entries

Network of associatons between targets according to the STRING database.

First level regulatory network of Lhx5_Lmx1b_Lhx1

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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
1.7	46.4	GO:0010880	regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum(GO:0010880)
0.2	34.5	GO:0006941	striated muscle contraction(GO:0006941)
1.4	25.0	GO:0032060	bleb assembly(GO:0032060)
7.8	23.5	GO:0002838	stimulatory C-type lectin receptor signaling pathway(GO:0002223) negative regulation of response to tumor cell(GO:0002835) negative regulation of immune response to tumor cell(GO:0002838) negative regulation of natural killer cell mediated immune response to tumor cell(GO:0002856) negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target(GO:0002859)
0.6	23.5	GO:0032814	regulation of natural killer cell activation(GO:0032814)
0.0	23.3	GO:0050911	detection of chemical stimulus involved in sensory perception of smell(GO:0050911)
0.2	21.8	GO:0007229	integrin-mediated signaling pathway(GO:0007229)
7.0	20.9	GO:0042706	eye photoreceptor cell fate commitment(GO:0042706) photoreceptor cell fate commitment(GO:0046552)
1.4	20.5	GO:0038094	Fc-gamma receptor signaling pathway(GO:0038094)
2.9	20.4	GO:2001015	negative regulation of skeletal muscle cell differentiation(GO:2001015)

Showing 1 to 10 of 169 entries

Gene overrepresentation in cellular component category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.2	49.1	GO:0009897	external side of plasma membrane(GO:0009897)
15.5	46.4	GO:0014801	longitudinal sarcoplasmic reticulum(GO:0014801)
0.3	43.5	GO:0030018	Z disc(GO:0030018)
7.6	38.0	GO:0005927	muscle tendon junction(GO:0005927)
0.1	31.3	GO:0005578	proteinaceous extracellular matrix(GO:0005578)
0.3	29.8	GO:0022625	cytosolic large ribosomal subunit(GO:0022625)
1.5	29.2	GO:0090665	dystrophin-associated glycoprotein complex(GO:0016010) glycoprotein complex(GO:0090665)
0.9	25.8	GO:0046930	pore complex(GO:0046930)
0.0	20.5	GO:0009986	cell surface(GO:0009986)
4.2	16.7	GO:0042585	germinal vesicle(GO:0042585) dendritic branch(GO:0044307)

Showing 1 to 10 of 84 entries

Gene overrepresentation in molecular function category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.6	41.8	GO:0005201	extracellular matrix structural constituent(GO:0005201)
3.9	27.5	GO:0030881	beta-2-microglobulin binding(GO:0030881)
1.2	26.1	GO:0004745	retinol dehydrogenase activity(GO:0004745)
1.1	25.8	GO:0015288	porin activity(GO:0015288)
0.2	24.6	GO:0001078	transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding(GO:0001078)
0.1	23.3	GO:0030246	carbohydrate binding(GO:0030246)
0.0	23.3	GO:0004984	olfactory receptor activity(GO:0004984)
0.1	20.8	GO:0003735	structural constituent of ribosome(GO:0003735)
4.3	17.1	GO:0004687	myosin light chain kinase activity(GO:0004687)
0.3	17.0	GO:0005080	protein kinase C binding(GO:0005080)

Showing 1 to 10 of 130 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	30.5	PID INSULIN GLUCOSE PATHWAY	Insulin-mediated glucose transport
0.2	14.8	PID FGF PATHWAY	FGF signaling pathway
0.2	12.5	PID TNF PATHWAY	TNF receptor signaling pathway
0.3	12.2	ST T CELL SIGNAL TRANSDUCTION	T Cell Signal Transduction
0.2	11.5	PID NOTCH PATHWAY	Notch signaling pathway
0.2	11.5	PID E2F PATHWAY	E2F transcription factor network
0.3	10.7	PID INTEGRIN A4B1 PATHWAY	Alpha4 beta1 integrin signaling events
0.3	8.5	PID AURORA A PATHWAY	Aurora A signaling
0.1	7.8	PID P53 REGULATION PATHWAY	p53 pathway
0.3	7.1	PID NFKAPPAB CANONICAL PATHWAY	Canonical NF-kappaB pathway

Showing 1 to 10 of 36 entries

Gene overrepresentation in curated gene sets: REACTOME pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.7	27.8	REACTOME STRIATED MUSCLE CONTRACTION	Genes involved in Striated Muscle Contraction
0.3	19.1	REACTOME COSTIMULATION BY THE CD28 FAMILY	Genes involved in Costimulation by the CD28 family
0.2	18.6	REACTOME PEPTIDE CHAIN ELONGATION	Genes involved in Peptide chain elongation
1.7	16.7	REACTOME REGULATION OF INSULIN SECRETION BY ACETYLCHOLINE	Genes involved in Regulation of Insulin Secretion by Acetylcholine
0.3	15.5	REACTOME INTERFERON GAMMA SIGNALING	Genes involved in Interferon gamma signaling
1.1	14.8	REACTOME FGFR2C LIGAND BINDING AND ACTIVATION	Genes involved in FGFR2c ligand binding and activation
0.1	12.7	REACTOME DOWNSTREAM SIGNALING EVENTS OF B CELL RECEPTOR BCR	Genes involved in Downstream Signaling Events Of B Cell Receptor (BCR)
0.8	11.5	REACTOME SYNTHESIS OF PIPS AT THE EARLY ENDOSOME MEMBRANE	Genes involved in Synthesis of PIPs at the early endosome membrane
0.2	9.3	REACTOME ION TRANSPORT BY P TYPE ATPASES	Genes involved in Ion transport by P-type ATPases
0.4	9.0	REACTOME OXYGEN DEPENDENT PROLINE HYDROXYLATION OF HYPOXIA INDUCIBLE FACTOR ALPHA	Genes involved in Oxygen-dependent Proline Hydroxylation of Hypoxia-inducible Factor Alpha

Showing 1 to 10 of 48 entries

Results for Lhx5_Lmx1b_Lhx1

Z-value: 0.85

Motif logo

Transcription factors associated with Lhx5_Lmx1b_Lhx1

Activity-expression correlation:

Activity profile of Lhx5_Lmx1b_Lhx1 motif

Sorted Z-values of Lhx5_Lmx1b_Lhx1 motif

Top targets:

Network of associatons between targets according to the STRING database.

First level regulatory network of Lhx5_Lmx1b_Lhx1

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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: