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 CALR
Basic gene info.Gene symbolCALR
Gene namecalreticulin
SynonymsCRT|HEL-S-99n|RO|SSA|cC1qR
CytomapUCSC genome browser: 19p13.3-p13.2
Genomic locationchr19 :13049413-13055304
Type of geneprotein-coding
RefGenesNM_004343.3,
Ensembl idENSG00000179218
DescriptionCRP55ERp60HACBPSicca syndrome antigen A (autoantigen Ro; calreticulin)calregulinendoplasmic reticulum resident protein 60epididymis secretory sperm binding protein Li 99ngrp60
Modification date20141222
dbXrefs MIM : 109091
HGNC : HGNC
Ensembl : ENSG00000179218
HPRD : 00169
Vega : OTTHUMG00000180574
ProteinUniProt: P27797
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CALR
BioGPS: 811
Gene Expression Atlas: ENSG00000179218
The Human Protein Atlas: ENSG00000179218
PathwayNCI Pathway Interaction Database: CALR
KEGG: CALR
REACTOME: CALR
ConsensusPathDB
Pathway Commons: CALR
MetabolismMetaCyc: CALR
HUMANCyc: CALR
RegulationEnsembl's Regulation: ENSG00000179218
miRBase: chr19 :13,049,413-13,055,304
TargetScan: NM_004343
cisRED: ENSG00000179218
ContextiHOP: CALR
cancer metabolism search in PubMed: CALR
UCL Cancer Institute: CALR
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of CALR in cancer cell metabolism1. Cleyrat C, Darehshouri A, Steinkamp MP, Vilaine M, Boassa D, et al. (2014) Mpl traffics to the cell surface through conventional and unconventional routes. Traffic 15: 961-982. doi: 10.1111/tra.12185. pmid: 4141020. go to article
2. Liu XL, Zhao D, Sun DP, Wang Y, Li Y, et al. (2012) Adenovirus-mediated delivery of CALR and MAGE-A3 inhibits invasion and angiogenesis of glioblastoma cell line U87. J Exp Clin Cancer Res 31: 8. doi: 10.1186/1756-9966-31-8. pmid: 3337230. go to article

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Phenotypic Information for CALR(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CALR
Familial Cancer Database: CALR
* 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 109091; gene.
Orphanet 3318; Essential thrombocythemia.
824; Myelofibrosis with myeloid metaplasia.
DiseaseKEGG Disease: CALR
MedGen: CALR (Human Medical Genetics with Condition)
ClinVar: CALR
PhenotypeMGI: CALR (International Mouse Phenotyping Consortium)
PhenomicDB: CALR

Mutations for CALR
* 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
ovaryCALRchr191305007813050098CALRchr191305268713052707
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 CALR related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE837730CALR4134191305089413051121MCM312627565213710052137249
BQ305064NME4119716449730450405CALR190533191305092413051448
CA425105RPLP22233811810303812873CALR333615191305158313054597
BU191818KIF18B1384174300379143005610CALR385913191304943513050937
AW615310GPR1152236964768940247689749CALR363559191305465813054854
BX501381RYR244491237794746237801769CALR444563191305518413055303
BF873592NDRG21131142148518721485317CALR129390191305434813054692
BE763150CALR1164191305160413054416CALR163228191305452513054590
D83840CALR156191305026113050316CALR52473191305032513051266
BQ304201CALR14206191305031313050926CALR203354191305092913051175
BG491927FAU20101116488817864888260CALR98950191305032813054606
BE005287OXSR11024833828424438289224CALR246380191305089513051124
AW367058CALR37431191305115613054375CALR427537191305436913054561
BE717818TENM433304117886079878861068CALR295453191305143213051680
C06296CALR156191305026113050316CALR52411191305032513051205
N39173CALR4342191305041713055301CALR341459191305036913050905

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=42)
Stat. for Synonymous SNVs
(# total SNVs=16)
Stat. for Deletions
(# total SNVs=1017)
Stat. for Insertions
(# total SNVs=492)

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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
chr19:13054565-13054616p.L367fs*46740
chr19:13054627-13054628p.K385fs*47433
chr19:13054564-13054615p.E364fs*46105
chr19:13054575-13054608p.K368fs*5111
chr19:13054568-13054613p.L367fs*4810
chr19:13054627-13054627p.K385fs*4710
chr19:13054567-13054612p.Q365fs*504
chr19:13054628-13054629p.E386fs*464
chr19:13054613-13054613p.E381fs*494
chr19:13054573-13054618p.L367fs*484

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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
# sample11 42 1 1  222  12 4
# mutation11 42 1 1  222  12 4
nonsynonymous SNV 1 1  1 1  1 1  12 3
synonymous SNV1  32      121     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
chr19:13054368p.L12F1
chr19:13050871p.S323F1
chr19:13054393p.L51V1
chr19:13051137p.I326I1
chr19:13054412p.K62R1
chr19:13051173p.D335N1
chr19:13054418p.G106G1
chr19:13049502p.E341G1
chr19:13051239p.Y128C1
chr19:13054427p.G343D1

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 CALR 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 CALR

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

ALG3,CALR,CRELD2,DDOST,DNAJB11,HSP90B1,HSPA5,
HYOU1,MANF,MED8,P4HB,PDIA3,PDIA3P1,PDIA4,
PDIA6,PPIB,PRDX4,PRKCSH,RPN1,SEC61A1,UQCRH
C19orf10,CALR,CNDP2,CNPY3,CORO1B,CRELD2,DNASE2,
GMPPB,SLC52A2,HM13,LMAN2,NANS,P4HB,PPIB,
RPN1,RRBP1,SDF2L1,SDF4,SLC39A1,SLC39A7,TMED9

C19orf10,CALR,CRELD2,ENO1,FKBP2,HSP90B1,HSPA5,
HYOU1,MANF,NUCB2,P4HB,PDIA3,PDIA3P1,PDIA4,
PDIA6,PGAM1,PKM,PPIB,RPN1,SDF2L1,TXNL4A
ASS1,BACE2,CALR,CRELD2,DNAJB11,ENO1,GMPPB,
HSPA5,HYOU1,LRRC59,MANF,NOS2,PDIA3,PDIA3P1,
PDIA4,PDIA6,PSMB2,PSMC4,RPN1,SDF2L1,TMED9
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 CALR
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA26046; -.
Organism-specific databasesCTD 811; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01065calreticulinapproved; nutraceuticalMelatonin
DB00864calreticulinapproved; investigationalTacrolimus


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Cross referenced IDs for CALR
* 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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