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 CALM1
Basic gene info.Gene symbolCALM1
Gene namecalmodulin 1 (phosphorylase kinase, delta)
SynonymsCALML2|CAMI|CPVT4|DD132|PHKD|caM
CytomapUCSC genome browser: 14q32.11
Genomic locationchr14 :90863326-90874619
Type of geneprotein-coding
RefGenesNM_006888.4,
NM_001166106.1,
Ensembl idENSG00000198668
Descriptioncalmodulinphosphorylase kinase, delta subunitprepro-calmodulin 1
Modification date20141222
dbXrefs MIM : 114180
HGNC : HGNC
Ensembl : ENSG00000198668
HPRD : 00241
Vega : OTTHUMG00000171044
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CALM1
BioGPS: 801
Gene Expression Atlas: ENSG00000198668
The Human Protein Atlas: ENSG00000198668
PathwayNCI Pathway Interaction Database: CALM1
KEGG: CALM1
REACTOME: CALM1
ConsensusPathDB
Pathway Commons: CALM1
MetabolismMetaCyc: CALM1
HUMANCyc: CALM1
RegulationEnsembl's Regulation: ENSG00000198668
miRBase: chr14 :90,863,326-90,874,619
TargetScan: NM_006888
cisRED: ENSG00000198668
ContextiHOP: CALM1
cancer metabolism search in PubMed: CALM1
UCL Cancer Institute: CALM1
Assigned class in ccmGDBC

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Phenotypic Information for CALM1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CALM1
Familial Cancer Database: CALM1
* 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: CALM1
MedGen: CALM1 (Human Medical Genetics with Condition)
ClinVar: CALM1
PhenotypeMGI: CALM1 (International Mouse Phenotyping Consortium)
PhenomicDB: CALM1

Mutations for CALM1
* 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
* 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
ovaryCALM1chr149086796190867981CALM1chr149086851890868538
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 CALM1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF898266CALM11169149086347490863532MINK1662701747910274793840
AI141454DCXR8305177999375779994181CALM1302372149087373190873801
BF218294CALM12235149087225390872488PSME3226318174099516340995255
BE765928IRF2BP2111851234741708234741882CALM1176266149087355690873646
BE813514CALM11391149087385290874245MGP385468121503495215035035
AW993959CALM11393149087385290874245MGP387470121503495215035035
AA496229CALM11152149087250290872653UNC5CL15251764102953341032107
BE813702CALM11387149087386190874245MGP381464121503495215035035
AW993976CALM11389149087385290874245MGP383466121503495215035035
CD366766CALM11154149087082090871147RALA15554573973000239745749
BE813534CALM11392149087385290874245MGP386469121503495215035035
AW993963CALM11389149087385290874245MGP383466121503495215035035
AW993962CALM11392149087385290874245MGP386469121503495215035035
AW993965CALM11390149087385290874245MGP384467121503495215035035
BE813679CALM11392149087385290874245MGP386469121503495215035035
BF949860CALM1278149087296690873043CANX741665179146676179146768
CB164141STAU139440204773006047730461CALM1429546149087114990871266
AI918711CALM11136149087082090871129CALM1128284149087196090872116
CB161392STAU139440204773006047730461CALM1429536149087114990871256
AA421615AIMP111924107268733107268924CALM1185394149087171490871923
AA652945CALM18465149087143790871892CALM1461553149087168590871777
AW502357CERS2202591150937735150937974CALM1250518149087221890872487
AA319858CACNA1B1919140952227140952317CALM189373149086640890870313
M78058FSCN1158756460115646068CALM159438149087132890871706
CB250526CALM11889149087109390871164ABI2826352204234195204234749
W26114CALM126236149087382190874031CALM1235510149087424090874517
CF891084CALM11889149087109390871164ABI2827612204234068204234749

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 # sample          2      
GAIN (# sample)          1      
LOSS (# sample)          1      
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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=11)
Stat. for Synonymous SNVs
(# total SNVs=4)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr14:90870756-90870756p.R107C3
chr14:90870237-90870237p.L70F2
chr14:90870757-90870757p.R107H2
chr14:90870246-90870246p.M73I1
chr14:90867643-90867643p.D25D1
chr14:90870251-90870251p.R75I1
chr14:90867659-90867659p.K31E1
chr14:90870298-90870298p.R91*1
chr14:90867678-90867678p.M37T1
chr14:90870303-90870303p.V92V1

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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
# sample11111 1 2  3    11 2
# mutation11111 1 2  3    11 1
nonsynonymous SNV1 1 1 1 2  2    11 1
synonymous SNV 1 1       1        
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
chr14:90870756p.R107C2
chr14:90870303p.R107H1
chr14:90866423p.D134N1
chr14:90870757p.N138S1
chr14:90867659p.T6T1
chr14:90870837p.K31E1
chr14:90867746p.G60S1
chr14:90870850p.P67L1
chr14:90870227p.P67P1
chr14:90870228p.L70F1

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 CALM1 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 CALM1

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

AHSA1,AKT1,ATP6V1D,C14orf1,GSKIP,CALM1,CCNK,
CPSF2,DLST,EIF2B2,ERH,GOLGA5,MARK3,MED6,
PPP2R5C,PSMA3,PSMC1,RDH11,SETD3,SMEK1,TTC9
ANGPT1,ANKRD40,BCAP29,BHMT2,CALM1,CAV1,EPDR1,
FAM69A,GNG2,ITGB1BP1,MAP2K1,PALMD,RHOQ,RTN4,
SAR1A,SEC23A,SH3GLB1,SORBS1,TTC7B,UGP2,YWHAG

ARF6,ATP6V1D,CALM1,EXOC5,FAM177A1,FKBP3,GLRX5,
GMFB,AP5M1,NUMB,PPM1A,PPP2R5E,PSEN1,SCFD1,
SETD3,SMEK1,SRP54,UBR7,VTI1B,WDR20,YY1
ACTB,ACTR1A,CA14,CALM1,CASQ1,CDC42EP4,CKMT2,
DGKG,FREM1,HRASLS,INPP5A,KCNK3,KCTD8,KLHL1,
MYOM2,NTM,PCP4L1,ARHGEF26,SLC8A1,SMYD1,TUBB2A
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 CALM1
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
DB00527calmodulin 1 (phosphorylase kinase, delta)approvedDibucaine
DB00622calmodulin 1 (phosphorylase kinase, delta)approvedNicardipine
DB00623calmodulin 1 (phosphorylase kinase, delta)approvedFluphenazine
DB00753calmodulin 1 (phosphorylase kinase, delta)approvedIsoflurane
DB00831calmodulin 1 (phosphorylase kinase, delta)approvedTrifluoperazine
DB00836calmodulin 1 (phosphorylase kinase, delta)approvedLoperamide
DB00850calmodulin 1 (phosphorylase kinase, delta)approvedPerphenazine
DB00925calmodulin 1 (phosphorylase kinase, delta)approvedPhenoxybenzamine
DB01023calmodulin 1 (phosphorylase kinase, delta)approved; investigationalFelodipine
DB01065calmodulin 1 (phosphorylase kinase, delta)approved; nutraceuticalMelatonin
DB01069calmodulin 1 (phosphorylase kinase, delta)approvedPromethazine
DB01100calmodulin 1 (phosphorylase kinase, delta)approvedPimozide
DB01115calmodulin 1 (phosphorylase kinase, delta)approvedNifedipine
DB01244calmodulin 1 (phosphorylase kinase, delta)approvedBepridil
DB01429calmodulin 1 (phosphorylase kinase, delta)approvedAprindine
DB02868calmodulin 1 (phosphorylase kinase, delta)experimental3''-(Beta-Chloroethyl)-2'',4''-Dioxo-3, 5''-Spiro-Oxazolidino-4-Deacetoxy-Vinblastine
DB03900calmodulin 1 (phosphorylase kinase, delta)experimental2-Methyl-2-Propanol
DB03977calmodulin 1 (phosphorylase kinase, delta)experimentalN-Trimethyllysine
DB04513calmodulin 1 (phosphorylase kinase, delta)experimentalN-(6-Aminohexyl)-5-Chloro-1-Naphthalenesulfonamide
DB04825calmodulin 1 (phosphorylase kinase, delta)withdrawnPrenylamine
DB04841calmodulin 1 (phosphorylase kinase, delta)approvedFlunarizine
DB08039calmodulin 1 (phosphorylase kinase, delta)experimental(3Z)-N,N-DIMETHYL-2-OXO-3-(4,5,6,7-TETRAHYDRO-1H-INDOL-2-YLMETHYLIDENE)-2,3-DIHYDRO-1H-INDOLE-5-SULFONAMIDE
DB08231calmodulin 1 (phosphorylase kinase, delta)experimentalMYRISTIC ACID
DB00360calmodulin 1 (phosphorylase kinase, delta)approved; investigationalTetrahydrobiopterin
DB00864calmodulin 1 (phosphorylase kinase, delta)approved; investigationalTacrolimus
DB00125calmodulin 1 (phosphorylase kinase, delta)approved; nutraceuticalL-Arginine
DB00435calmodulin 1 (phosphorylase kinase, delta)approvedNitric Oxide


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Cross referenced IDs for CALM1
* 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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