Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 AMN
Basic gene info.Gene symbolAMN
Gene nameamnion associated transmembrane protein
SynonymsPRO1028|amnionless
CytomapUCSC genome browser: 14q32.3
Genomic locationchr14 :103388992-103397179
Type of geneprotein-coding
RefGenesNM_030943.3,
Ensembl idENSG00000166126
Descriptionamnionless homologprotein amnionlessvisceral endoderm-specific type 1 transmembrane protein
Modification date20141207
dbXrefs MIM : 605799
HGNC : HGNC
Ensembl : ENSG00000166126
HPRD : 09314
Vega : OTTHUMG00000171897
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_AMN
BioGPS: 81693
Gene Expression Atlas: ENSG00000166126
The Human Protein Atlas: ENSG00000166126
PathwayNCI Pathway Interaction Database: AMN
KEGG: AMN
REACTOME: AMN
ConsensusPathDB
Pathway Commons: AMN
MetabolismMetaCyc: AMN
HUMANCyc: AMN
RegulationEnsembl's Regulation: ENSG00000166126
miRBase: chr14 :103,388,992-103,397,179
TargetScan: NM_030943
cisRED: ENSG00000166126
ContextiHOP: AMN
cancer metabolism search in PubMed: AMN
UCL Cancer Institute: AMN
Assigned class in ccmGDBC

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Phenotypic Information for AMN(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: AMN
Familial Cancer Database: AMN
* 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_LIPIDS_AND_LIPOPROTEINS
REACTOME_LIPOPROTEIN_METABOLISM

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

Mutations for AMN
* 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
ovaryAMNchr14103391119103391139RCOR1chr14103135072103135092
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 AMN related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=10)
Stat. for Synonymous SNVs
(# total SNVs=8)
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
chr14:103395144-103395144p.P115P3
chr14:103395162-103395162p.G121G2
chr14:103390133-103390133p.C43*2
chr14:103390137-103390137p.G45S1
chr14:103395248-103395248p.F150S1
chr14:103390157-103390157p.P51P1
chr14:103395294-103395294p.S165S1
chr14:103389034-103389034p.V3V1
chr14:103390271-103390271p.?1
chr14:103395498-103395498p.S185Y1

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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
# sample 1 2    4   1   41 1
# mutation 1 2    4   1   31 1
nonsynonymous SNV 1 1    2   1   2  1
synonymous SNV   1    2       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
chr14:103389067p.C14C2
chr14:103395162p.G121G2
chr14:103395248p.G448R1
chr14:103396268p.A33T1
chr14:103396997p.P51P1
chr14:103390101p.S67T1
chr14:103390157p.D74N1
chr14:103390308p.G82G1
chr14:103394775p.D131N1
chr14:103394801p.R134H1

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 AMN 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 AMN

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

AIM1L,ALDH3A1,AMN,BCL2L10,C4orf17,CDX2,CHP2,
CRYBB2,DUOXA2,FAM83C,GAST,GPX2,ID1,IQCF2,
KLC3,LOC285629,NMB,RBMXL2,SNHG12,SOX21,VCX3A
ACSM2A,ACSM2B,AMN,APOC3,APOL4,BMP3,TBATA,
CHGA,CHGB,DBH,NDRG4,NTSR2,ORM1,ORM2,
PDZD7,PHOX2B,SLC18A1,SNORA14A,ST8SIA3,TH,TTC36

ACADS,ACBD4,AMN,ANKRD9,LMNTD2,TMEM253,EXOC3L4,
CDC42EP5,ELMO3,GSTZ1,ITM2C,ITPK1,LDHD,LOC115110,
MARVELD3,NOXA1,P2RX4,PEX11G,POLD4,SLC25A1,TMEM54
AMN,SOWAHA,CDHR5,CES2,CYP27A1,CYP4F12,DCAF11,
DHRS11,FAM109A,GDPD2,INPP5J,IYD,KIAA2013,MEP1A,
MYO1A,RAB17,SLC39A5,SLC9A3R1,TMEM120A,TNNC2,USH1C
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 AMN
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00200amnion associated transmembrane proteinapprovedHydroxocobalamin


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Cross referenced IDs for AMN
* 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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