More Gene Info

[Identification] [Functional Reference] [Interactions] [Signal Transduction Pathways] [Transcripts]
[Homology Group] [Affymetrix Probe Sets] [Gene Ontology] [Cancers (COSMIC)] [Chemical Entities of Biological Interest (ChEBI)] [External Databases]

This page presents information relevant for one locus, which is identified by its unique Genomatix LocusID. The data includes information collected from a number of publicly available sources as well as Genomatix curated data.

Identification & Functional Information

Identification and Functional Information shows the Genomatix LocusID, the official or preferred gene name and gene symbol from EntrezGene, synonyms etc. For genes identified as transcription factor, the binding site description from the MatInspector matrix library is listed (if available).
A click on the "Genome Browser" image will open the Genomatix Genome Browser preloaded with the selected locus.

Example:

Identification
LocusID	GXL_316835
Name	hepatocyte nuclear factor 4, alpha
Protein Name	hepatocyte nuclear factor 4 alpha,HNF4alpha10/11/12,transcription factor-14,hepatic nuclear factor 4 alpha
Symbol	HNF4A
Synonyms	FLJ39654, HNF4, HNF4A, HNF4a7, HNF4a8, HNF4a9, HNF4alpha, MODY, MODY1, NR2A1, NR2A21, TCF, TCF14, hepatic nuclear factor 4alpha , hepatocyte nuclear factor (HNF)-4alpha, hepatocyte nuclear factor 4alpha, Hepatocyte Nuclear Factor 4{alpha}, hepatocyte nuclear factor-4, Hepatocyte nuclear factor-4alpha, maturity-onset diabetes of the young
Organism	Homo sapiens (human)
Chromosomal Location	20q12-q13.1
GeneID	3172
Unigene Cluster	Hs.116462
	Identified as Transcription Factor. DNA binding sites are described by V$NR2F.

Functional Information
The protein encoded by this gene is a nuclear transcription factor which binds DNA as a homodimer. The encoded protein controls the expression of several genes, including hepatocyte nuclear factor 1 alpha, a transcription factor which regulates the expression of several hepatic genes. This gene may play a role in development of the liver, kidney, and intestines. Mutations in this gene have been associated with monogenic autosomal dominant non-insulin-dependent diabetes mellitus type I. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq]

Functional Information

The protein encoded by this gene is a nuclear transcription factor which binds DNA as a homodimer. The encoded protein controls the expression of several genes, including hepatocyte nuclear factor 1 alpha, a transcription factor which regulates the expression of several hepatic genes. This gene may play a role in development of the liver, kidney, and intestines. Mutations in this gene have been associated with monogenic autosomal dominant non-insulin-dependent diabetes mellitus type I. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq]

Functional Reference

Functional Reference provides a list of manually curated references to PubMed relevant for this gene. The data is extracted from GeneRIF (NCBI)

Example:

Functional Reference
Observational study of gene-disease association. (HuGE Navigator)
Control transcription of aldehyde dehydrogenase 2
HNF4 alpha activates the insulin gene directly, through a previously unrecognized cis element
HNF-4alpha is involved in regulating cancer cell transmigration by modulating the Fas-FasL system
mutations in maturity-onset diabetes of the young (MODY) candidate genes in 22 Spanish families.
...

Interactions

If available, interactions between genes and transcription factors are displayed. These interactions have been extracted manually from PubMed abstracts by Genomatix experts. The table shows the type of the interaction (e.g. activating), the sentences of the PubMed abstracts from which the information has been derived from as well as a link to the complete PubMed abstracts.

Example:

Interactions
Genes	Type	Description	Citation
CEBPA cooperates with HNF4A	-	Using different molecular approaches, we demonstrate that hepatocyte nuclear factor (HNF4alpha), CAAT/enhancer-binding protein-alpha (C/EBPalpha), C/EBPbeta, and cAMP response element-binding protein (CREB) are involved in the potentiated PKA responsiveness: in the distal region, via one HNF4alpha- and one C/EBP-binding sites, and in the proximal region, via two HNF4alpha and two CREB-binding sites.
PPARGC1A regulates HNF4A	-	The coactivator PGC-1 enhanced transcriptional activity of HNF-4, and this enhancement was suppressed by rifampicin-activated PXR.
CREB1 cooperates with HNF4A	-	Using different molecular approaches, we demonstrate that hepatocyte nuclear factor (HNF4alpha), CAAT/enhancer-binding protein-alpha (C/EBPalpha), C/EBPbeta, and cAMP response element-binding protein (CREB) are involved in the potentiated PKA responsiveness: in the distal region, via one HNF4alpha- and one C/EBP-binding sites, and in the proximal region, via two HNF4alpha and two CREB-binding sites. These data strongly suggest that the cAMP responsiveness of the Glc6Pase promoter requires a tight cooperation between a proximal and a distal region, which depends on the presence of several HNF4alpha-, C/EBP-, and CREB-binding sites, therefore involving an intricate association of hepatic and ubiquitous transcription factors.
...

Signal Transduction Pathway Associations

If available, signal transduction pathway associations extracted by LitInspector are displayed. The table shows the number of PubMed references where these pathway associations are described and links to graphical pathway representations of BioCarta, KEGG, and STKE.

Example:

Signal Transduction Pathway associations and potential interactions
Ref.	Pathway Component	Signaling Pathway
10	MAPK	mitogen activated protein kinase signaling (BioCarta BioCarta BioCarta BioCarta BioCarta STKE STKE KEGG)
9	INS	insulin signaling (BioCarta)
5	PPARA	peroxisome proliferative activated receptor alpha signaling (BioCarta BioCarta KEGG)
5	TGF BETA	tgf beta signaling (BioCarta BioCarta STKE KEGG)
4	NFKB	nf kappa b signaling (BioCarta)
...

Transcripts

All transcripts of the gene which have been mapped to the genomic sequences are listed. Redundant transcripts sharing an identical exon/intron structure with an other transcript are marked respectivly. They are only listed here and can not be accessed in Eldorado. The table shows the Genomatix transcript ID, the accession number of the mapped cDNA sequence and the description of the cDNA sequence.
A click on the "TViewer" image will open the Genomatix Transcriptome Viewer preloaded with the selected locus.

Example:

Transcripts
TranscriptID	cDNA Accession	Description
GXT_22544954	XM_001110097	Transcript derived from mapping of the cdna XM_001110097 from mml
GXT_2815203	NM_178850	Homo sapiens hepatocyte nuclear factor 4, alpha (HNF4A), transcript variant 3, mRNA. This variant (3) includes an alternate segment compared to variant 2, that causes a frameshift. The resulting isoform (c) is shorter and has a distinct C-terminus compared to isoform b.
GXT_2807165	NM_178849	Homo sapiens hepatocyte nuclear factor 4, alpha (HNF4A), transcript variant 1, mRNA. This variant (1) uses an alternate in-frame splice site in the 3' coding region compared to variant 2, resulting in a shorter isoform (a) compared to isoform b.
GXT_21914753	NM_175914	Homo sapiens hepatocyte nuclear factor 4, alpha (HNF4A), transcript variant 4, mRNA. This variant (4) also known as variant 8, differs in the 5' UTR and has multiple coding region differences, compared to variant 2. These differences cause translation initiation at an upstream AUG and an isoform (d) with a shorter N-terminus compared to isoform b.
...

Homology Group

All genes in the Genomatix homology group of the input genes are listed.

Example:

Homology Group Hg25393
Organism	LocusID	Symbol	Description	GeneID
Macaca mulatta (rhesus monkey)	GXL_553011	LOC717972	similar to hepatocyte nuclear factor 4 alpha isoform a	717972
Canis lupus familiaris (dog)	GXL_337846	HNF4A	hepatocyte nuclear factor 4, alpha	485884
Danio rerio (zebrafish)	GXL_528771	hnf4a	hepatocyte nuclear factor 4, alpha	322358
Mus musculus (mouse)	GXL_120457	Hnf4a	hepatic nuclear factor 4, alpha	15378
Rattus norvegicus (rat)	GXL_21050	Hnf4a	hepatocyte nuclear factor 4, alpha	25735
Pan troglodytes (chimp)	GXL_778141	HNF4A	hepatocyte nuclear factor 4, alpha	458269
Bos taurus (cow)	GXL_503650	HNF4A	hepatocyte nuclear factor 4, alpha	509200
Gallus gallus (chicken)	GXL_611999	HNF4A	hepatocyte nuclear factor 4, alpha	419198
Taeniopygia guttata (zebra finch)	GXL_864927	LOC100221920	similar to hepatocyte nuclear factor 4 alpha	100221920
Equus caballus (horse)	GXL_681304	HNF4A	hepatocyte nuclear factor 4, alpha	100056007
Monodelphis domestica (opossum)	GXL_699302	LOC100023834	similar to hepatocyte nuclear factor 4alpha	100023834
Sus scrofa (pig)	GXL_771630	HNF4A	hepatocyte nuclear factor 4, alpha	733636
Homo sapiens (human)	GXL_316835	HNF4A	hepatocyte nuclear factor 4, alpha	3172

Affymetrix Probe Sets

Probe Sets from several Affymetrix chips which could be mapped to this locus are displayed. The table shows the Genomatix transcript ID and the probe sets of which at least one individual probe is located in the transcript. The number of the single probes that could be mapped to the transcript is given by the first number in the column "Matching Probes". The second number indicates how many probes of the probe set could be mapped to the genome without a mismatch.

Example:

Affymetrix Probe Sets
TranscriptID	Probe Set	Chip	Matching Probes
GXT_2815203	208429_PM_x_at	Human Genome Array Plate	5 / 9
GXT_2815203	36722_s_at	Human Genome U95Av2	3 / 16
GXT_2815203	X87871_s_at	Human Genome FL (6800)	8 / 20
GXT_2815203	208429_x_at	Human Genome U133A, Human Genome U133A 2.0, Human Genome U133 Plus 2.0	6 / 11
GXT_2815203	11738423_a_at	Human Genome U219 Plate	11 / 11
...

Gene Ontology

If this locus has a GeneID which is annotated with terms from Gene Ontology (GO), these term are displayed together with a PubMed reference for supporting evidence:

Example:

Gene Ontology
Category	Term	Evidence	Citation
molecular_function	transcription factor activity	inferred from direct assay
molecular_function	steroid hormone receptor activity	inferred from electronic annotation
molecular_function	receptor binding	inferred from direct assay
molecular_function	steroid binding	inferred from electronic annotation
molecular_function	fatty acid binding	inferred from direct assay
...

If further ontological annotations are available, they are displayed in a similar fashion:

Example:

Further Annotation
Category	Term	Evidence	Citation
cellular role	Pol II transcription	not recorded
biochemical function	Receptor (signalling)	not recorded
subcellular localization	Nuclear	not recorded
organismal role	Blood clotting	not recorded

Cancers (COSMIC)

Gene associations with cancer tissues obtained from the Sanger Institute Catalogue Of Somatic Mutations In Cancer web site, http://www.sanger.ac.uk/cosmic
Bamford et al (2004) The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. Br J Cancer, 91,355-358.
For information on redistributing this data please see http://www.sanger.ac.uk/genetics/CGP/cosmic/disclaimer.shtml

Example:

Cancers (COSMIC)
Primary Tissue	Sub Tissue	Histology	Sub Histology	CDS Mutation	AA Mutation	Pubmed Id
lung	NS	carcinoma	adenocarcinoma
	NS	carcinoma	non_small_cell_carcinoma
	NS	carcinoma	NS	c.146A>T	p.N49I
	NS	carcinoma	small_cell_carcinoma
ovary	NS	carcinoma	serous_carcinoma	c.1179G>A	p.L393L	PubMed link
pancreas	NS	carcinoma	ductal_carcinoma
	NS	carcinoma	ductal_carcinoma			PubMed link
	NS	carcinoma	NS	c.387C>T	p.A129A
...

Chemical Entities of Biological Interest (ChEBI)

Gene associations with chemical entities obtained from the ChEBI web site, http://www.ebi.ac.uk/chebi
de Matos, P., Alcántara, R., Dekker, A., Ennis, M., Hastings, J., Haug, K., Spiteri, I., Turner, S., and Steinbeck, C. (2009). Chemical entities of biological interest: an update. Nucleic Acids Res.

Example:

Chemical Entities of Biological Interest (ChEBI)
ChEBI ID	ChEBI name	XREF source	XREF ID	XREF name	Definition
35475	non-steroidal anti-inflammatory drug	NCI	C257	nsaids	An anti-inflammatory drug that is not a steroid. In addition to anti-inflammatory actions, non-steroidal anti-inflammatory drugs have analgesic, antipyretic, and platelet-inhibitory actions. They act by blocking the synthesis of prostaglandins by inhibiting cyclooxygenase, which converts arachidonic acid to cyclic endoperoxides, precursors of prostaglandins.
35475	non-steroidal anti-inflammatory drug	ONT	-	-
35480	analgesic	ONT	-	-	An agent capable of relieving pain without the loss of consciousness or without producing anaesthesia. In addition, analgesic is a role played by a compound which is exhibited by a capability to cause a reduction of pain symptoms.
35481	non-narcotic analgesic	ONT	-	-	A drug that has principally analgesic, antipyretic and anti-inflammatory actions. Non-narcotic analgesics do not bind to opioid receptors.
35493	antipyretic	ONT	-	-	A drug that prevents or reduces fever by lowering the body temperature from a raised state. An antipyretic will not affect the normal body temperature if one does not have fever. Antipyretics cause the hypothalamus to override an interleukin-induced increase in temperature. The body will then work to lower the temperature and the result is a reduction in fever.
35544	cyclooxygenase inhibitor	NCI	C1323	cyclooxygenase inhibitor	A compound or agent that combines with cyclooxygenases and thereby prevents its substrate-enzyme combination with arachidonic acid and the formation of eicosanoids, prostaglandins, and thromboxanes.
35544	cyclooxygenase inhibitor	ONT	-	-
...

External Databases

If there is information available in external databases, additional links to these databases are supplied.

Example:

Links to External Databases
EntrezGene dbSNP for GeneID 3172 Ensembl for GeneID 3172 UniGene for Hs.116462 HomoloGene for GeneID 3172 Genomatix Literature Analysis (gene-gene cocitations) KEGG OMIM