Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for HNRNPD
Basic gene info.Gene symbolHNRNPD
Gene nameheterogeneous nuclear ribonucleoprotein D (AU-rich element RNA binding protein 1, 37kDa)
SynonymsAUF1|AUF1A|HNRPD|P37|hnRNPD0
CytomapUCSC genome browser: 4q21
Genomic locationchr4 :83274466-83295149
Type of geneprotein-coding
RefGenesNM_001003810.1,
NM_002138.3,NM_031369.2,NM_031370.2,
Ensembl idENSG00000138668
DescriptionARE-binding protein AUFI, type Aheterogeneous nuclear ribonucleoprotein D0hnRNP D0
Modification date20141207
dbXrefs MIM : 601324
HGNC : HGNC
HPRD : 03206
ProteinUniProt: Q14103
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HNRNPD
BioGPS: 3184
Gene Expression Atlas: ENSG00000138668
The Human Protein Atlas: ENSG00000138668
PathwayNCI Pathway Interaction Database: HNRNPD
KEGG: HNRNPD
REACTOME: HNRNPD
ConsensusPathDB
Pathway Commons: HNRNPD
MetabolismMetaCyc: HNRNPD
HUMANCyc: HNRNPD
RegulationEnsembl's Regulation: ENSG00000138668
miRBase: chr4 :83,274,466-83,295,149
TargetScan: NM_001003810
cisRED: ENSG00000138668
ContextiHOP: HNRNPD
cancer metabolism search in PubMed: HNRNPD
UCL Cancer Institute: HNRNPD
Assigned class in ccmGDBB - This gene belongs to cancer gene.

Top
Phenotypic Information for HNRNPD(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HNRNPD
Familial Cancer Database: HNRNPD
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_MRNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM 601324; gene.
601324; gene.
Orphanet
DiseaseKEGG Disease: HNRNPD
MedGen: HNRNPD (Human Medical Genetics with Condition)
ClinVar: HNRNPD
PhenotypeMGI: HNRNPD (International Mouse Phenotyping Consortium)
PhenomicDB: HNRNPD

Mutations for HNRNPD
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryHNRNPDchr48328590483285924HNRNPDchr48328596583285985
pancreasHNRNPDchr48328256183282581chr48329554183295561
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows HNRNPD related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a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check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample        1        
GAIN (# sample)        1        
LOSS (# sample)                 
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

Top
check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=1

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=19)
Stat. for Synonymous SNVs
(# total SNVs=5)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

Top
check002.gifTop 10 SNVs Having the Most Samples in COSMIC data
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.
GRCh37 positionMutation(aa)Unique sampleID count
chr4:83278594-83278594p.E209*2
chr4:83277754-83277754p.Y312Y1
chr4:83278498-83278498p.E241*1
chr4:83280703-83280703p.T127I1
chr4:83277757-83277757p.G311G1
chr4:83278499-83278499p.M240I1
chr4:83280713-83280713p.V124I1
chr4:83277828-83277828p.Q288E1
chr4:83278508-83278508p.K237N1
chr4:83294618-83294618p.K72*1

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample11 6    1  2 1   1 5
# mutation11 6    1  2 1   1 5
nonsynonymous SNV11 5    1  1     1 4
synonymous SNV   1       1 1     1
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

Top
check002.gifTop 10 SNVs Having the Most Samples in TCGA data
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.
Genomic PositionMutation(aa)Unique sampleID count
chr4:83277757p.R261C,HNRNPD1
chr4:83279905p.R253K,HNRNPD1
chr4:83277964p.M239V,HNRNPD1
chr4:83280703p.C233C,HNRNPD1
chr4:83277987p.H226R,HNRNPD1
chr4:83280713p.K223N,HNRNPD1
chr4:83278030p.K218N,HNRNPD1
chr4:83278046p.E190K,HNRNPD1
chr4:83278485p.L170I,HNRNPD1
chr4:83278493p.P161P,HNRNPD1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for HNRNPD in TCGA
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

Top
Gene Expression for HNRNPD

check002.gifGene Expression in Cancer Cell-lines (CCLE)
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

check002.gifDifferential Gene Expression in Primary Tumors (TCGA)
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
Gene-Gene Network Information
check002.gifCo-Expressed gene's network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

ANP32B,CDCA3,EXOSC9,GAR1,H2AFZ,HMGB2,HNRNPA2B1,
HNRNPD,HNRNPL,LYAR,MAGOH,MND1,NASP,PTMA,
SFPQ,SRSF3,SRSF7,SNRPD1,SNRPG,STMN1,TARDBP
DDX27,DKC1,DNAJC9,FUS,GAR1,HNRNPD,HNRNPM,
HNRNPU,NOP58,OCIAD2,POLR1C,PRPF4,PSPC1,PTPN2,
RPP38,SNRPD1,SSRP1,TACSTD2,TRIM26,UMPS,UTP3

EWSR1,FEN1,FUS,HMGB2,HNRNPA2B1,HNRNPA3,HNRNPD,
HNRNPR,HNRNPU,HNRNPDL,KPNB1,NASP,NCAPH,NCL,
PAICS,PLK4,SFPQ,SRSF1,SNRPA,TAF15,TARDBP
BMS1,DDX46,DHX29,DHX9,EIF4G1,ELAVL1,EWSR1,
FTSJ3,FUS,HNRNPA3,HNRNPD,HNRNPM,HNRNPR,HNRNPU,
NCL,NUP188,SLC7A1,SRRM1,SYNCRIP,TAF15,TARDBP
check002.gifCo-Expressed gene's Protein-protein interaction Network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for HNRNPD


There's no related Drug.
Top
Cross referenced IDs for HNRNPD
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas