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 PAM16
Basic gene info.Gene symbolPAM16
Gene namepresequence translocase-associated motor 16 homolog (S. cerevisiae)
SynonymsMAGMAS|TIM16|TIMM16
CytomapUCSC genome browser: 16p13.3
Genomic locationchr16 :4390251-4401373
Type of geneprotein-coding
RefGenesNM_016069.9,
Ensembl idENSG00000217930
Descriptionmagmas-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 date20141207
dbXrefs MIM : 614336
HGNC : HGNC
Ensembl : ENSG00000217930
HPRD : 14798
Vega : OTTHUMG00000129466
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PAM16
BioGPS: 51025
Gene Expression Atlas: ENSG00000217930
The Human Protein Atlas: ENSG00000217930
PathwayNCI Pathway Interaction Database: PAM16
KEGG: PAM16
REACTOME: PAM16
ConsensusPathDB
Pathway Commons: PAM16
MetabolismMetaCyc: PAM16
HUMANCyc: PAM16
RegulationEnsembl's Regulation: ENSG00000217930
miRBase: chr16 :4,390,251-4,401,373
TargetScan: NM_016069
cisRED: ENSG00000217930
ContextiHOP: PAM16
cancer metabolism search in PubMed: PAM16
UCL Cancer Institute: PAM16
Assigned class in ccmGDBC

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Phenotypic Information for PAM16(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PAM16
MedGen: PAM16 (Human Medical Genetics with Condition)
ClinVar: PAM16
PhenotypeMGI: PAM16 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PAM16 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA612149PAM1612211643909654401294TSPAN3219558157734655177348599
AA829953LPXN8236115829434458294572PAM162334951643948104395072

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

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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=2

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check002.gifSomatic 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.

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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
chr16:4390379-4390379p.E107*2
chr16:4390398-4390398p.R100R2
chr16:4393215-4393215p.E27D1
chr16:4390324-4390324p.T125M1
chr16:4393222-4393222p.R25Q1
chr16:4390345-4390346p.E118fs*>81
chr16:4393259-4393259p.V13M1
chr16:4390365-4390365p.I111M1
chr16:4393260-4393260p.G12G1
chr16:4390368-4390368p.K110N1

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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=0

Point Mutation/ Tissue ID1234567891011121314151617181920
# 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])

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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

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 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]

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Gene Expression for PAM16

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

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
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 PAM16


There's no related Drug.
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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



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