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 CALM3
Basic gene info.Gene symbolCALM3
Gene namecalmodulin 3 (phosphorylase kinase, delta)
SynonymsHEL-S-72|PHKD|PHKD3
CytomapUCSC genome browser: 19q13.2-q13.3
Genomic locationchr19 :47104511-47114039
Type of geneprotein-coding
RefGenesNM_005184.2,
Ensembl idENSG00000160014
DescriptioncaMcalmodulinepididymis secretory protein Li 72prepro-calmodulin 3
Modification date20141207
dbXrefs MIM : 114183
HGNC : HGNC
Ensembl : ENSG00000160014
HPRD : 00243
Vega : OTTHUMG00000133517
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CALM3
BioGPS: 808
Gene Expression Atlas: ENSG00000160014
The Human Protein Atlas: ENSG00000160014
PathwayNCI Pathway Interaction Database: CALM3
KEGG: CALM3
REACTOME: CALM3
ConsensusPathDB
Pathway Commons: CALM3
MetabolismMetaCyc: CALM3
HUMANCyc: CALM3
RegulationEnsembl's Regulation: ENSG00000160014
miRBase: chr19 :47,104,511-47,114,039
TargetScan: NM_005184
cisRED: ENSG00000160014
ContextiHOP: CALM3
cancer metabolism search in PubMed: CALM3
UCL Cancer Institute: CALM3
Assigned class in ccmGDBC

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Phenotypic Information for CALM3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CALM3
Familial Cancer Database: CALM3
* 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_CARBOHYDRATES
REACTOME_GLUCOSE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: CALM3
MedGen: CALM3 (Human Medical Genetics with Condition)
ClinVar: CALM3
PhenotypeMGI: CALM3 (International Mouse Phenotyping Consortium)
PhenomicDB: CALM3

Mutations for CALM3
* 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 CALM3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE930858PPAP2B2016615700497757005126CALM3165388194711219147112551
BQ327040CALM35123194711318447113304TROVE21174001193057032193057310
BF947810CADM362251159172123159172343CALM3219419194711304047113240
BU931140COL18A118553214693310146933634CALM3553674194710457647104696
M86171CALM31140194711355747113696CALM3136350194710458447111524
BF802907CALM313191194711277547112954DDX5181430176249695162497200
AW867517CALM315215194711174447112203MSN212600X6496079964961187
BI028359CALM327196194711173747112165CALM3191308194711220047112460
BF839329CALM313168194711119147111347ANKRD26160225102736942127369486
AK124456CALM38021116194711351047113824CALM311112170194711261247114038
BQ327094CALM3994194711318447113269TROVE2883211193057032193057265
AI760114CALM316378194711367747114039SCN3A3704472166043719166043797
BG979974SPINT114146154114968841149827CALM3137404194711218147112592
AW895034CELSR211851109817969109818153CALM3186305194711221547112477
T05484NCAM119011113094797113094887CALM391232194711151247111794

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=5)
Stat. for Synonymous SNVs
(# total SNVs=3)
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
chr19:47112393-47112393p.M145V1
chr19:47112395-47112395p.M145I1
chr19:47109107-47109107p.Q9H1
chr19:47111488-47111488p.D23E1
chr19:47111507-47111507p.T30S1
chr19:47111527-47111527p.V36V1
chr19:47111798-47111801p.D81fs*281
chr19:47111800-47111800p.T80T1
chr19:47112130-47112130p.E105Q1
chr19:47112165-47112165p.K116K1

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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  11  1    1 1   1 2
# mutation  11  1    1 1   1 2
nonsynonymous SNV  11  1      1   1  
synonymous SNV           1       2
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
chr19:47109107p.Q9H1
chr19:47111527p.V36V1
chr19:47111573p.M52V1
chr19:47111779p.M73I1
chr19:47112165p.K116K1
chr19:47112210p.I131I1
chr19:47112393p.M145V1
chr19:47112395p.M145I1

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 CALM3 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 CALM3

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

AP2S1,BCKDHA,CALM3,CCDC9,EPN1,EXOSC5,GRWD1,
GSK3A,LIG1,NOSIP,PAFAH1B3,PPFIA3,PPP5C,PRKD2,
RUVBL2,SAE1,SNRPD2,STRN4,SYMPK,TFPT,UBE2S
AP2S1,ARPC1B,ATP6V0D1,KIAA0930,CALM3,CNPY3,CTSD,
CTSZ,CYBA,GRN,IFI30,ITGB2,LSP1,MAN2B1,
NAGK,NAGPA,PLA2G15,PLD3,PNPLA6,TYROBP,VPS18

ALDH16A1,AP2S1,BCAT2,CALM3,CNDP2,GSG2,GYS1,
LIG1,MBOAT7,MCM5,PFKP,PFN1,PIH1D1,POLD1,
PPP5C,PRKD2,RNF19B,PPP6R1,TYMS,VRK3,YIF1B
APOL1,APOL2,CALM3,CFB,EPSTI1,ETV7,GBP2,
GZMA,IRF9,MDK,NUB1,PARP9,PSMB9,PSME1,
PSME2,RARRES3,STAT1,TAP1,TAP2,TRAFD1,UBE2L6
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 CALM3
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
DB00360calmodulin 3 (phosphorylase kinase, delta)approved; investigationalTetrahydrobiopterin
DB00864calmodulin 3 (phosphorylase kinase, delta)approved; investigationalTacrolimus
DB00125calmodulin 3 (phosphorylase kinase, delta)approved; nutraceuticalL-Arginine
DB00435calmodulin 3 (phosphorylase kinase, delta)approvedNitric Oxide


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Cross referenced IDs for CALM3
* 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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