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 KIFC3

Basic gene info.	Gene symbol	KIFC3
	Gene name	kinesin family member C3
	Synonyms	-
	Cytomap	UCSC genome browser: 16q13-q21
	Genomic location	chr16 :57792128-57831929
	Type of gene	protein-coding
	RefGenes	NM_001130099.1, NM_001130100.1,NM_005550.3,
	Ensembl id	ENSG00000269180
	Description	kinesin-like protein KIFC3
	Modification date	20141207
dbXrefs	MIM : 604535
	HGNC : HGNC
	Ensembl : ENSG00000140859
	HPRD : 05171
	Vega : OTTHUMG00000133455
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_KIFC3
	BioGPS: 3801
	Gene Expression Atlas: ENSG00000269180
	The Human Protein Atlas: ENSG00000269180
Pathway	NCI Pathway Interaction Database: KIFC3
	KEGG: KIFC3
	REACTOME: KIFC3
	ConsensusPathDB
	Pathway Commons: KIFC3
Metabolism	MetaCyc: KIFC3
	HUMANCyc: KIFC3
Regulation	Ensembl's Regulation: ENSG00000269180
	miRBase: chr16 :57,792,128-57,831,929
	TargetScan: NM_001130099
	cisRED: ENSG00000269180
Context	iHOP: KIFC3
	cancer metabolism search in PubMed: KIFC3
	UCL Cancer Institute: KIFC3
Assigned class in ccmGDB	C

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Phenotypic Information for KIFC3(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: KIFC3
	Familial Cancer Database: KIFC3

* 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_PROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: KIFC3
	MedGen: KIFC3 (Human Medical Genetics with Condition)
	ClinVar: KIFC3
Phenotype	MGI: KIFC3 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: KIFC3

Mutations for KIFC3

* 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

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- For Intra-chromosomal Variations

There's no intra-chromosomal structural variation.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
breast	KIFC3	chr16	57810327	57810327	KCNJ6	chr21	39130447	39130447

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 KIFC3 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
BM726297	KIFC3	1	69	16	57792333	57792401	CANX	69	495	5	179157500	179157926
BM680904	CANX	19	445	5	179157500	179157926	KIFC3	445	498	16	57792333	57792386
BE715187	LAMB3	15	101	1	209791887	209791973	KIFC3	95	265	16	57818591	57818761
CV355096	KIFC3	5	377	16	57806598	57806970	INSR	368	587	19	7227814	7228036

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=47)	Stat. for Synonymous SNVs (# total SNVs=11)

Stat. for Deletions (# total SNVs=2)	Stat. for Insertions (# total SNVs=1)

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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
chr16:57804520-57804520	p.V286V	2
chr16:57804546-57804546	p.R278W	2
chr16:57799532-57799532	p.R451C	2
chr16:57794781-57794781	p.I697V	2
chr16:57793712-57793712	p.R802W	2
chr16:57794238-57794238	p.R775C	2
chr16:57799480-57799480	p.A468V	1
chr16:57805300-57805300	p.A192V	1
chr16:57794247-57794247	p.P772T	1
chr16:57803505-57803505	p.?	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=2

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				10	1		1			1		5	1	2	1		2	6		7
# mutation				11	1		1			1		6	1	2	1		3	7		9
nonsynonymous SNV				9	1							6		2	1		3	6		9
synonymous SNV				2			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
chr16:57799532	p.R312C,KIFC3	2
chr16:57805117	p.A555S,KIFC3	1
chr16:57794744	p.I204V,KIFC3	1
chr16:57828936	p.V65V,KIFC3	1
chr16:57799480	p.T528K,KIFC3	1
chr16:57805181	p.I119S,KIFC3	1
chr16:57794777	p.P52P,KIFC3	1
chr16:57829005	p.T499T,KIFC3	1
chr16:57799526	p.P114H,KIFC3	1
chr16:57805259	p.P46H,KIFC3	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 KIFC3 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 KIFC3

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


PXDC1,CCDC102A,COL18A1,FAM20C,FHL3,KIFC3,LCAT, LMNA,MAP7D1,MGAT1,PDLIM2,PDLIM7,PLEKHM2,PPM1F, PRKCDBP,PTGIR,RAB3IL1,RIN3,SERPINH1,SPHK1,TUBB6	ASCC2,DBNL,EGLN2,EML3,FES,FURIN,INF2, KANK3,KIFC3,LRFN4,LZTR1,LZTS2,NUCB1,PHLDA3, PKN1,PPP1R12C,RNH1,RNPEPL1,RPS6KA4,TAOK2,ZDHHC8

BMP1,CERCAM,CFH,CHST15,COL18A1,COL6A2,GNAI2, KIFC3,LAMB2,LATS2,LEPRE1,LOXL1,MAP7D1,MAPK11, MMP14,MRC2,NXN,PRKCDBP,SLC12A4,TSPAN4,UBTD1	ABCD1,ANGPTL4,CDR2L,CITED1,DFNA5,FTCD,HOXC11, KIFC3,MAOB,MGC45800,PHYHIPL,PMP22,RHOBTB2,SEC14L2, SFRP5,SFXN3,SH3GL1,SLC16A4,SUSD2,TIAM2,TMEM25

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 KIFC3

There's no related Drug.

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Cross referenced IDs for KIFC3

* 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