Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	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 symbol	HNRNPD
	Gene name	heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA binding protein 1, 37kDa)
	Synonyms	AUF1\|AUF1A\|HNRPD\|P37\|hnRNPD0
	Cytomap	UCSC genome browser: 4q21
	Genomic location	chr4 :83274466-83295149
	Type of gene	protein-coding
	RefGenes	NM_001003810.1, NM_002138.3,NM_031369.2,NM_031370.2,
	Ensembl id	ENSG00000138668
	Description	ARE-binding protein AUFI, type Aheterogeneous nuclear ribonucleoprotein D0hnRNP D0
	Modification date	20141207
dbXrefs	MIM : 601324
	HGNC : HGNC
	HPRD : 03206
Protein	UniProt: Q14103 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_HNRNPD
	BioGPS: 3184
	Gene Expression Atlas: ENSG00000138668
	The Human Protein Atlas: ENSG00000138668
Pathway	NCI Pathway Interaction Database: HNRNPD
	KEGG: HNRNPD
	REACTOME: HNRNPD
	ConsensusPathDB
	Pathway Commons: HNRNPD
Metabolism	MetaCyc: HNRNPD
	HUMANCyc: HNRNPD
Regulation	Ensembl's Regulation: ENSG00000138668
	miRBase: chr4 :83,274,466-83,295,149
	TargetScan: NM_001003810
	cisRED: ENSG00000138668
Context	iHOP: HNRNPD
	cancer metabolism search in PubMed: HNRNPD
	UCL Cancer Institute: HNRNPD
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM	601324; gene. 601324; gene.
Orphanet
Disease	KEGG Disease: HNRNPD
	MedGen: HNRNPD (Human Medical Genetics with Condition)
	ClinVar: HNRNPD
Phenotype	MGI: HNRNPD (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	HNRNPD	chr4	83285904	83285924	HNRNPD	chr4	83285965	83285985
pancreas	HNRNPD	chr4	83282561	83282581		chr4	83295541	83295561

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows HNRNPD related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
BF096106	NFE2L2	16	213	2	178096309	178096506	HNRNPD	209	575	4	83275272	83278599
BE646088	HNRNPD	17	136	4	83275139	83275258	VAMP2	134	339	17	8063452	8063657
AA010774	LAMB2	1	183	3	49162488	49162755	HNRNPD	180	232	4	83275291	83275343
DA569517	RILPL2	1	613	12	123907633	123921017	HNRNPD	613	761	4	83280731	83294626
BU632297	NHP2L1	19	171	22	42070813	42070965	HNRNPD	170	646	4	83278036	83280793
DB050538	HNRNPD	1	96	4	83295053	83295148	ELL	93	567	19	18554825	18555299
BM835099	HNRNPD	1	282	4	83294848	83295133	NOL6	276	447	9	33465827	33466171
BF096260	PDCD10	337	359	3	167446609	167446632	HNRNPD	350	625	4	83276455	83277976
BF805251	PPDPF	1	142	20	62152884	62153103	HNRNPD	133	360	4	83278003	83279861
BE935692	GRHL2	51	76	8	102629161	102629189	HNRNPD	61	241	4	83284033	83284211
BF096098	PDCD10	337	359	3	167446609	167446632	HNRNPD	350	625	4	83276455	83277976
BG999638	HNRNPD	5	318	4	83293008	83293322	HNRNPD	305	448	4	83284057	83284200
BG988244	HNRNPD	4	291	4	83275185	83275470	TMEM67	292	518	8	94828925	94829151
DA845763	RASGRF1	1	242	15	79296310	79298561	HNRNPD	227	563	4	83294752	83295087
BF805263	PPDPF	12	142	20	62152884	62153092	HNRNPD	133	360	4	83278003	83279861

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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)

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SNV 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

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Somatic 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.

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Top 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 position	Mutation(aa)	Unique sampleID count
chr4:83278594-83278594	p.E209*	2
chr4:83278485-83278485	p.H245R	1
chr4:83279905-83279905	p.K176N	1
chr4:83277695-83277695	p.Y332C	1
chr4:83278493-83278493	p.K242N	1
chr4:83280638-83280638	p.E149*	1
chr4:83277705-83277705	p.Y329H	1
chr4:83278494-83278495	p.K242fs*8	1
chr4:83280677-83280677	p.R136*	1
chr4:83277754-83277754	p.Y312Y	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1	1		6					1			2		1				1		5
# mutation	1	1		6					1			2		1				1		5
nonsynonymous SNV	1	1		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])

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Top 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 Position	Mutation(aa)	Unique sampleID count
chr4:83278594	p.S283N,HNRNPD	1
chr4:83277695	p.T108I,HNRNPD	1
chr4:83279868	p.R276S,HNRNPD	1
chr4:83277754	p.V105I,HNRNPD	1
chr4:83279893	p.Y313C,HNRNPD	1
chr4:83277757	p.Y293Y,HNRNPD	1
chr4:83279905	p.G292G,HNRNPD	1
chr4:83277964	p.R261C,HNRNPD	1
chr4:83280703	p.R253K,HNRNPD	1
chr4:83277987	p.M239V,HNRNPD	1

Other 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

Copy 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]

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Gene Expression for HNRNPD

Gene 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.

Differential 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))

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CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

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Gene-Gene Network Information

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting Genes (from Pathway Commons)

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

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Pharmacological Information for HNRNPD

There's no related Drug.

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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