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

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 PAM16

Basic gene info.	Gene symbol	PAM16
	Gene name	presequence translocase-associated motor 16 homolog (S. cerevisiae)
	Synonyms	MAGMAS\|TIM16\|TIMM16
	Cytomap	UCSC genome browser: 16p13.3
	Genomic location	chr16 :4390251-4401373
	Type of gene	protein-coding
	RefGenes	NM_016069.9,
	Ensembl id	ENSG00000217930
	Description	magmas-like proteinmitochondria associated protein involved in granulocyte macrophage colony stimulating factor signal transductionmitochondria-associated granulocyte macrophage CSF-signaling moleculemitochondrial import inner membrane translocase subu
	Modification date	20141207
dbXrefs	MIM : 614336
	HGNC : HGNC
	Ensembl : ENSG00000217930
	HPRD : 14798
	Vega : OTTHUMG00000129466
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PAM16
	BioGPS: 51025
	Gene Expression Atlas: ENSG00000217930
	The Human Protein Atlas: ENSG00000217930
Pathway	NCI Pathway Interaction Database: PAM16
	KEGG: PAM16
	REACTOME: PAM16
	ConsensusPathDB
	Pathway Commons: PAM16
Metabolism	MetaCyc: PAM16
	HUMANCyc: PAM16
Regulation	Ensembl's Regulation: ENSG00000217930
	miRBase: chr16 :4,390,251-4,401,373
	TargetScan: NM_016069
	cisRED: ENSG00000217930
Context	iHOP: PAM16
	cancer metabolism search in PubMed: PAM16
	UCL Cancer Institute: PAM16
Assigned class in ccmGDB	C

Top

Phenotypic Information for PAM16(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PAM16
	Familial Cancer Database: PAM16

* 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: PAM16
	MedGen: PAM16 (Human Medical Genetics with Condition)
	ClinVar: PAM16
Phenotype	MGI: PAM16 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PAM16

Mutations for PAM16

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PAM16 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
DA612149	PAM16	1	221	16	4390965	4401294	TSPAN3	219	558	15	77346551	77348599
AA829953	LPXN	8	236	11	58294344	58294572	PAM16	233	495	16	4394810	4395072

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

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

There's no copy number variation information in COSMIC data for this gene.

Top

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=2

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=8)	Stat. for Synonymous SNVs (# total SNVs=4)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	There's no inserted snv.

Top

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
chr16:4390379-4390379	p.E107*	2
chr16:4390398-4390398	p.R100R	2
chr16:4391407-4391407	p.L63F	1
chr16:4391481-4391481	p.R38Q	1
chr16:4391505-4391505	p.A30G	1
chr16:4393215-4393215	p.E27D	1
chr16:4390324-4390324	p.T125M	1
chr16:4393222-4393222	p.R25Q	1
chr16:4390345-4390346	p.E118fs*>8	1
chr16:4393259-4393259	p.V13M	1

Top

SNV Counts per Each Loci in TCGA data

: non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=0

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
# mutation
nonsynonymous SNV
synonymous SNV

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

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

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 PAM16 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 PAM16

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))

Top

CNV 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

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


BCL7C,BOLA2,C16orf13,TSR3,PPP1R35,FAM173A,FAM195A, INO80E,MPG,MRPL28,MRPL55,MRPS34,NDUFB10,NME3, NMRAL1,NUBP2,PGP,RPUSD1,STUB1,TCEB2,PAM16	ALKBH7,ANAPC11,ATP5D,C19orf70,CLPP,COX4I1,ECI1, FAM195A,HSF1,MRPL12,MRPL38,MRPS24,NDUFA13,NDUFB11, PHPT1,PLEKHJ1,PPP1R16A,TCEB2,PAM16,TIMM17B,TIMM50

ANAPC11,ATP5J2,C16orf13,FAM195A,FAM96B,FAU,GADD45GIP1, LSM7,MRPL11,NDUFA11,NDUFA13,NDUFA2,NDUFB10,NDUFB7, NUBP2,NUTF2,RPL35,PAM16,TMEM223,UQCRQ,ZNF593	ABT1,C16orf91,CECR5,CYC1,DNAJA3,FLAD1,GTPBP8, MRPL57,MRPL11,MRPL54,MRPS12,MRPS7,NXT1,PSMG3, SF3B5,STOML2,TARBP2,PAM16,TMEM223,TOMM22,WDR61

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

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

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

Top

Pharmacological Information for PAM16

There's no related Drug.

Top

Cross referenced IDs for PAM16

* 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