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 KIF13A
Basic gene info.Gene symbolKIF13A
Gene namekinesin family member 13A
SynonymsRBKIN|bA500C11.2
CytomapUCSC genome browser: 6p23
Genomic locationchr6 :17950636-17987854
Type of geneprotein-coding
RefGenesNM_001105566.2,
NM_001105567.2,NM_001105568.2,NM_001243423.1,NM_022113.5,
Ensembl idENSG00000137177
Descriptionhomolog of mouse KIF13A mannose-6-phosphate receptor transporterkinesin-like protein KIF13Akinesin-like protein RBKIN
Modification date20141207
dbXrefs MIM : 605433
HGNC : HGNC
Ensembl : ENSG00000137177
HPRD : 09256
Vega : OTTHUMG00000014313
ProteinUniProt: Q9H1H9
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_KIF13A
BioGPS: 63971
Gene Expression Atlas: ENSG00000137177
The Human Protein Atlas: ENSG00000137177
PathwayNCI Pathway Interaction Database: KIF13A
KEGG: KIF13A
REACTOME: KIF13A
ConsensusPathDB
Pathway Commons: KIF13A
MetabolismMetaCyc: KIF13A
HUMANCyc: KIF13A
RegulationEnsembl's Regulation: ENSG00000137177
miRBase: chr6 :17,950,636-17,987,854
TargetScan: NM_001105566
cisRED: ENSG00000137177
ContextiHOP: KIF13A
cancer metabolism search in PubMed: KIF13A
UCL Cancer Institute: KIF13A
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for KIF13A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: KIF13A
Familial Cancer Database: KIF13A
* 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 STAD 6,

Therapeutic Vulnerabilities in Cancer7

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,
6 http://www.nature.com/nature/journal/v513/n7517/full/nature13480.html,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM 605433; gene.
605433; gene.
Orphanet
DiseaseKEGG Disease: KIF13A
MedGen: KIF13A (Human Medical Genetics with Condition)
ClinVar: KIF13A
PhenotypeMGI: KIF13A (International Mouse Phenotyping Consortium)
PhenomicDB: KIF13A

Mutations for KIF13A
* 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
ovaryKIF13Achr61795617817956198KIF13Achr61794939017949410
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 KIF13A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ428394KIAA019512375177349455573495376KIF13A36767161776066917760973
T07391BZW2114471674600116746144KIF13A13430661796536417965643
BF001556TBC1D9B12155179289743179289957KIF13A21058861782600717828603
BF357666KIF13A123961783134317834305KIF13A23632061782610917826296
AW993933HEATR5B1747223724412637244584KIF13A45547961788879417888823

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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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)

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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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=111)		Stat. for Synonymous SNVs
(# total SNVs=48)
Stat. for Deletions
(# total SNVs=3)		Stat. for Insertions
(# total SNVs=1)

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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
chr6:17780996-17780996p.R1271R4
chr6:17856348-17856348p.E76*2
chr6:17817375-17817375p.R626W2
chr6:17849677-17849677p.A254E2
chr6:17781450-17781450p.S1209S2
chr6:17779187-17779187p.R1361R2
chr6:17764731-17764731p.A1676A2
chr6:17794560-17794560p.V1048I2
chr6:17804706-17804706p.F780L2
chr6:17779188-17779188p.R1361Q2

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample982216 3 72 13441 198 18
# mutation994226 5 82 16541 209 23
nonsynonymous SNV782163 4 62 13231 138 12
synonymous SNV21263 1 2  331  71 11
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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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
chr6:17850652p.K1268K,KIF13A2
chr6:17779188p.A254V,KIF13A2
chr6:17831438p.G432E,KIF13A2
chr6:17834246p.R207G,KIF13A2
chr6:17764967p.G1550S,KIF13A2
chr6:17855836p.K404N,KIF13A2
chr6:17849677p.F780F,KIF13A2
chr6:17780964p.R1348Q,KIF13A2
chr6:17804706p.S109F,KIF13A2
chr6:17777546p.S106S,KIF13A1

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 KIF13A 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 KIF13A

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))
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check002.gifCNV 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
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

AHNAK,APC,ASXL2,CREBRF,CCNT1,EP300,EXOC6B,
FNIP1,GIGYF2,GTF2A1,KIAA1109,KIF13A,PJA2,RAPGEF6,
REST,TGFBRAP1,TTBK2,UHMK1,ZBTB37,ZKSCAN8,ZXDA		APOOL,ATE1,CLASP1,DCAF5,DMD,DPP8,GOLGA4,
HECTD1,HERC1,HIPK3,KIAA0368,VWA8,KIF13A,LOC729082,
PRKAR2A,SLC25A46,USP24,USP25,USP9X,ZAK,ZFYVE9

AFF1,ANKFY1,NOP9,DENND4A,DYNC1H1,EP300,EYA3,
GTF2A1,HEATR5A,HIVEP1,KIF13A,LDOC1L,LRIG3,LUZP1,
MTF1,REST,RNF168,RREB1,YLPM1,ZNF106,ZNF407		ARVCF,BCL9,SOGA1,CELSR2,CHD6,CLTCL1,CROCCP3,
EPHA4,FAM63B,GPR161,HIP1,KIF13A,MTMR12,NFIX,
PKD1,RAI1,REV3L,SCN9A,TBC1D24,TTBK2,USP13
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

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check002.gifInteracting 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 KIF13A


There's no related Drug.
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Cross referenced IDs for KIF13A
* 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



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