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 SI
Basic gene info.Gene symbolSI
Gene namesucrase-isomaltase (alpha-glucosidase)
Synonyms-
CytomapUCSC genome browser: 3q25.2-q26.2
Genomic locationchr3 :164696685-164796283
Type of geneprotein-coding
RefGenesNM_001041.3,
Ensembl idENSG00000090402
Descriptionoligosaccharide alpha-1,6-glucosidasesucrase-isomaltase, intestinal
Modification date20141207
dbXrefs MIM : 609845
HGNC : HGNC
Ensembl : ENSG00000090402
HPRD : 01962
Vega : OTTHUMG00000158065
ProteinUniProt: P14410
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SI
BioGPS: 6476
Gene Expression Atlas: ENSG00000090402
The Human Protein Atlas: ENSG00000090402
PathwayNCI Pathway Interaction Database: SI
KEGG: SI
REACTOME: SI
ConsensusPathDB
Pathway Commons: SI
MetabolismMetaCyc: SI
HUMANCyc: SI
RegulationEnsembl's Regulation: ENSG00000090402
miRBase: chr3 :164,696,685-164,796,283
TargetScan: NM_001041
cisRED: ENSG00000090402
ContextiHOP: SI
cancer metabolism search in PubMed: SI
UCL Cancer Institute: SI
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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

check002.gifOthers
OMIM 222900; phenotype.
609845; gene.
Orphanet 306436; Congenital sucrase-isomaltase deficiency with starch intolerance.
306446; Congenital sucrase-isomaltase deficiency with minimal starch tolerance.
306462; Congenital sucrase-isomaltase deficiency without starch intolerance.
306474; Congenital sucrase-isomaltase deficiency with starch and lactose intolerance.
306486; Congenital sucrase-isomaltase deficiency without sucrose intolerance.
DiseaseKEGG Disease: SI
MedGen: SI (Human Medical Genetics with Condition)
ClinVar: SI
PhenotypeMGI: SI (International Mouse Phenotyping Consortium)
PhenomicDB: SI

Mutations for SI
* 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
pancreasSIchr3164768063164768263SIchr3164761867164762067
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 SI related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF907120SI2412693164723644164723672IFIH12693742163128764163128869

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 1              
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=8

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=416)
Stat. for Synonymous SNVs
(# total SNVs=62)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=4)

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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
chr3:164737556-164737556p.W1086*10
chr3:164786967-164786967p.R91T5
chr3:164785145-164785145p.K206K4
chr3:164764781-164764781p.P579S4
chr3:164737500-164737500p.R1105C4
chr3:164783091-164783091p.W255*4
chr3:164767590-164767590p.P529L4
chr3:164785146-164785146p.K206R3
chr3:164735642-164735642p.T1180T3
chr3:164741402-164741402p.R1019C3

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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=8

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample781264 34 12 2733513 16122128
# mutation781284 40 12 2984513 18227165
nonsynonymous SNV571212 30 10 2784213  6517 56
synonymous SNV21 72 10 2  203  1171019
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
chr3:164785145p.K206K4
chr3:164785146p.R250C3
chr3:164783108p.G125A3
chr3:164786619p.K206R3
chr3:164724636p.R3I2
chr3:164776753p.A436T2
chr3:164733000p.G1476E2
chr3:164725726p.R1019C2
chr3:164750471p.A1332V2
chr3:164741406p.R205R2

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 SI 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 SI

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

AKAP8,ANO8,BRD4,C19orf44,CC2D1A,CCDC130,CHERP,
DCAF15,DDA1,ELL,GTPBP3,MAU2,MED26,MRI1,
MYO9B,RFX1,SIN3B,TSSK6,TYK2,WIZ,YJEFN3
ABCC10,ANKRD11,CEP164,CUL9,GIGYF1,MAU2,ZSWIM8,
LENG8,MAPK8IP3,MBD1,MINK1,MYO15B,NEURL4,NISCH,
PGS1,RTEL1,SIN3B,TAF1C,TUBGCP6,ZNF335,ZNF646

AKAP8L,BRD4,SOGA1,CCDC130,COLQ,CRTC1,CUL9,
DOCK6,ELL,MAU2,MLLT1,MYO9B,NISCH,PKD1,
PPP1R12C,SEMA6C,SIN3B,SYNGAP1,TYK2,WIZ,ZNF333
ASXL1,ATXN2,PRRC2B,CEP164,CHD6,CRAMP1L,GIGYF1,
INTS3,L3MBTL1,LZTR1,NISCH,OBSCN,PPT2,SETD5,
SFSWAP,SIN3B,SSH1,SYNGAP1,ZC3H7B,ZDHHC8,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 SI
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P14410; -.
ChemistryChEMBL CHEMBL2748; -.
Organism-specific databasesPharmGKB PA35758; -.
Organism-specific databasesCTD 6476; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00284sucrase-isomaltase (alpha-glucosidase)approved; investigationalAcarbose
DB00747sucrase-isomaltase (alpha-glucosidase)approvedScopolamine
DB04465sucrase-isomaltase (alpha-glucosidase)experimentalLactose


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Cross referenced IDs for SI
* 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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