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 POM121
Basic gene info.Gene symbolPOM121
Gene namePOM121 transmembrane nucleoporin
SynonymsP145|POM121A
CytomapUCSC genome browser: 7q11.23
Genomic locationchr7 :72361471-72418843
Type of geneprotein-coding
RefGenesNM_001257190.2,
NM_172020.4,
Ensembl idENSG00000262122
DescriptionPOM121 membrane glycoproteinnuclear envelope pore membrane protein POM 121nuclear envelope pore membrane protein POM 121Anuclear pore membrane protein 121 kDanucleoporin Nup121
Modification date20141207
dbXrefs MIM : 615753
HGNC : HGNC
Ensembl : ENSG00000196313
HPRD : 11448
Vega : OTTHUMG00000023527
ProteinUniProt: Q96HA1
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_POM121
BioGPS: 9883
Gene Expression Atlas: ENSG00000262122
The Human Protein Atlas: ENSG00000262122
PathwayNCI Pathway Interaction Database: POM121
KEGG: POM121
REACTOME: POM121
ConsensusPathDB
Pathway Commons: POM121
MetabolismMetaCyc: POM121
HUMANCyc: POM121
RegulationEnsembl's Regulation: ENSG00000262122
miRBase: chr7 :72,361,471-72,418,843
TargetScan: NM_001257190
cisRED: ENSG00000262122
ContextiHOP: POM121
cancer metabolism search in PubMed: POM121
UCL Cancer Institute: POM121
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for POM121(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: POM121
Familial Cancer Database: POM121
* 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_NON_CODING_RNA
REACTOME_METABOLISM_OF_RNA
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM 615753; gene.
615753; gene.
Orphanet
DiseaseKEGG Disease: POM121
MedGen: POM121 (Human Medical Genetics with Condition)
ClinVar: POM121
PhenotypeMGI: POM121 (International Mouse Phenotyping Consortium)
PhenomicDB: POM121

Mutations for POM121
* 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
* 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.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryPOM121chr77239314872393168NCOR2chr12124842957124842977
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 POM121 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF528396TAPBPL14541265740566579811POM12145579077241994172420735
BM715257POM121135877238386072384217POM12135861177238503772385290

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 # sample1                
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=7

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=58)
Stat. for Synonymous SNVs
(# total SNVs=20)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=3)

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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
chr7:72413896-72413896p.T857A7
chr7:72413423-72413423p.P699L6
chr7:72413874-72413874p.N849N5
chr7:72413443-72413443p.A706T4
chr7:72413243-72413243p.H639P4
chr7:72412427-72412427p.S367N3
chr7:72413626-72413626p.G767S2
chr7:72416721-72416721p.P968Q2
chr7:72413539-72413539p.P738T2
chr7:72413673-72413673p.F782L2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample43283 4 22 362 1119116
# mutation43273 4 22 362 11410120
nonsynonymous SNV33162 1 21 342 1128113
synonymous SNV1 111 3  1  2   22 7
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
chr7:72398976p.N94S,POM1213
chr7:72413634p.T769T,POM1212
chr7:72413673p.F782F,POM1212
chr7:72397386p.R982H2
chr7:72416763p.A38T,POM1212
chr7:72411388p.P877S,POM1211
chr7:72413685p.T46I,POM1211
chr7:72397411p.S199F,POM1211
chr7:72413338p.P671S,POM1211
chr7:72413956p.E905K,POM1211

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 POM121 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 POM121

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

PRRC2A,BAZ1B,BLM,DNMT1,EIF4H,GTF2I,HCFC1,
KCTD7,LMTK2,NUP205,POM121,POM121C,RBM33,SBDSP1,
STAG3L1,STAG3L2,STAG3L3,TRRAP,XRCC2,ZC3HAV1L,ZSCAN25
ASXL1,BAZ2A,HECTD4,DNAH1,DNHD1,EP300,LINC01000,
HPS4,INTS3,MED12,NBPF9,NKTR,NUP214,POM121,
POM121C,RAD54L2,RBM33,SETD5,SPEN,SRRM2,USP49

BAZ1B,EIF4H,GCC1,GIGYF1,LMTK2,NOM1,PAXIP1,
POM121,POM121C,RBM33,SLC12A9,TAF6,TNPO3,TRIM56,
TRRAP,TYW1,UBN2,USP42,ZKSCAN5,ZSCAN25,ZNF746
ANKRD11,ATXN2L,BRPF1,CHERP,GCN1L1,KIAA0355,MDN1,
KMT2B___KMT2D,MYBBP1A,NUP214,POM121,POM121C,SAFB2,SNAPC4,
SRRM2,SYMPK,TUBGCP6,USP36,UTRN,ZMIZ2,ZNF142
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 POM121


There's no related Drug.
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Cross referenced IDs for POM121
* 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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