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More Gene Info


[Identification] [References] [Interactions] [Pathways] [Transcripts]
[Homology] [Affymetrix] [Gene Ontology] [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 GenomeBrowser
LocusID GXL_316835
Name hepatocyte nuclear factor 4, alpha
Protein Name hepatocyte nuclear factor 4-alpha,TCF-14,HNF4alpha10/11/12,transcription factor 14,transcription factor HNF-4,hepatic nuclear factor 4 alpha,nuclear receptor subfamily 2 group A member 1
Symbol HNF4A
Synonyms 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
Organism Homo sapiens (human)
Chromosomal Location 20q13.12
GeneID at NCBI 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]


References

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


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.

Additionally, a link to all gene-gene co-citations from the Genomatix Literature Mining is available (will open a new window).

Example:

To see all gene-gene co-citations for this gene: Genomatix Literature Analysis
Gene-TF interactions (based on Genomatix' PubMed Literature Mining, 2013-11-19)
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.
PubMed Link
PPARGC1A regulates HNF4A -
  • The coactivator PGC-1 enhanced transcriptional activity of HNF-4, and this enhancement was suppressed by rifampicin-activated PXR.
PubMed Link
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.
PubMed Link
...


Pathways

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 as well as links to graphical pathway representations of BioCarta, KEGG, and STKE.

Example:

Signal Transduction Pathway associations and potential interactions
Ref.Pathway ComponentSignaling Pathway
10MAPKmitogen activated protein kinase signaling (BioCarta BioCarta BioCarta BioCarta BioCarta STKE STKE KEGG)
9INSinsulin signaling (BioCarta)
5PPARAperoxisome proliferative activated receptor alpha signaling (BioCarta BioCarta KEGG)
5TGF BETAtgf beta signaling (BioCarta BioCarta STKE KEGG)
4NFKBnf 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, the description of the cDNA sequence, and the Pfam family.
A click on the "TViewer" image will open the Genomatix Transcriptome Viewer preloaded with the selected locus.

Example:

TranscriptsTranscriptomeViewer
TranscriptID cDNA Accession Description Pfam family
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.
Hormone_recep  |  zf-C4
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.
Hormone_recep  |  zf-C4
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.
Hormone_recep  |  zf-C4
GXT_24881729 NM_001258355 Homo sapiens hepatocyte nuclear factor 4, alpha (HNF4A), transcript variant 7, mRNA
This variant (7) contains an alternate coding exon compared to variant 2, that causes a frameshift. The resulting isoform (g) has a shorter and distinct N-terminus compared to isoform b.
Hormone_recep  |  zf-C4
...


Homology

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 HNF4A hepatocyte nuclear factor 4, alpha 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
Oryctolagus cuniculus (rabbit) GXL_1216151 LOC100345457 hepatocyte nuclear factor 4 alpha 100345457
Sus scrofa (pig) GXL_1621880 HNF4A hepatocyte nuclear factor 4, alpha 733636
Rattus norvegicus (rat) GXL_21050 Hnf4a hepatocyte nuclear factor 4, alpha 25735
Gallus gallus (chicken) GXL_611999 HNF4A hepatocyte nuclear factor 4, alpha 419198
Pan troglodytes (chimp) GXL_1786092 HNF4A hepatocyte nuclear factor 4, alpha 458269
Taeniopygia guttata (zebra finch) GXL_864927 HNF4A hepatocyte nuclear factor 4, alpha 100221920
Bos taurus (cow) GXL_1431578 HNF4A hepatocyte nuclear factor 4, alpha 509200
Equus caballus (horse) GXL_681304 HNF4A hepatocyte nuclear factor 4, alpha 100056007
Monodelphis domestica (opossum) GXL_699302 HNF4A hepatocyte nuclear factor 4, alpha 100023834
Homo sapiens (human) GXL_316835 HNF4A hepatocyte nuclear factor 4, alpha 3172
Xenopus tropicalis (western clawed frog) GXL_1261572 hnf4a hepatocyte nuclear factor 4, alpha 100492541


Affymetrix

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 PubMed Link
molecular_function steroid hormone receptor activity inferred from electronic annotation  
molecular_function receptor binding inferred from direct assay PubMed Link
molecular_function steroid binding inferred from electronic annotation  
molecular_function fatty acid binding inferred from direct assay PubMed Link
...


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 PubMed Link
biochemical function Receptor (signalling) not recorded PubMed Link
subcellular localization Nuclear not recorded PubMed Link
organismal role Blood clotting not recorded PubMed Link


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
UniGene for Hs.116462
HomoloGene for GeneID 3172
OMIM