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 SACM1L
Basic gene info.Gene symbolSACM1L
Gene nameSAC1 suppressor of actin mutations 1-like (yeast)
SynonymsSAC1
CytomapUCSC genome browser: 3p21.3
Genomic locationchr3 :45730753-45786900
Type of geneprotein-coding
RefGenesNM_014016.3,
Ensembl idENSG00000211456
Descriptionphosphatidylinositide phosphatase SAC1suppressor of actin 1suppressor of actin mutations 1-like protein
Modification date20141215
dbXrefs MIM : 606569
HGNC : HGNC
Ensembl : ENSG00000211456
HPRD : 07587
Vega : OTTHUMG00000156653
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SACM1L
BioGPS: 22908
Gene Expression Atlas: ENSG00000211456
The Human Protein Atlas: ENSG00000211456
PathwayNCI Pathway Interaction Database: SACM1L
KEGG: SACM1L
REACTOME: SACM1L
ConsensusPathDB
Pathway Commons: SACM1L
MetabolismMetaCyc: SACM1L
HUMANCyc: SACM1L
RegulationEnsembl's Regulation: ENSG00000211456
miRBase: chr3 :45,730,753-45,786,900
TargetScan: NM_014016
cisRED: ENSG00000211456
ContextiHOP: SACM1L
cancer metabolism search in PubMed: SACM1L
UCL Cancer Institute: SACM1L
Assigned class in ccmGDBC

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Phenotypic Information for SACM1L(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SACM1L
Familial Cancer Database: SACM1L
* 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_PHOSPHOLIPID_METABOLISM
REACTOME_PI_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SACM1L
MedGen: SACM1L (Human Medical Genetics with Condition)
ClinVar: SACM1L
PhenotypeMGI: SACM1L (International Mouse Phenotyping Consortium)
PhenomicDB: SACM1L

Mutations for SACM1L
* 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
pancreasSACM1Lchr34574165345741673chr36695778066957800
pancreasSACM1Lchr34576835145768371SACM1Lchr34576866745768687
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 SACM1L related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA761308WDR4317822913653629136613SACM1L7952034573092745751067
CB410891LINC004781444211762395517624398SACM1L44052834578608045786168
CA949726SACM1L19134578110745785085SACM1L8754834578507745785538

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 # sample3  2  1   1  2  1
GAIN (# sample)3  2  1   1  1  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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=33)
Stat. for Synonymous SNVs
(# total SNVs=8)
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
chr3:45780149-45780149p.D488N5
chr3:45779136-45779136p.Y434F3
chr3:45746676-45746676p.I60M2
chr3:45751048-45751048p.F131S2
chr3:45780132-45780132p.Y482C2
chr3:45773632-45773632p.Q363H1
chr3:45746631-45746631p.K45N1
chr3:45780148-45780148p.S487S1
chr3:45785048-45785048p.A551T1
chr3:45751121-45751121p.E155D1

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample11 7  3 12 121 215 2
# mutation11 7  3 12 321 215 2
nonsynonymous SNV11 4  1  2 32  1 3 1
synonymous SNV   3  2 1    1 112 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
chr3:45751048p.F131S2
chr3:45745000p.R35S2
chr3:45780364p.H65N1
chr3:45746628p.D488D1
chr3:45761023p.K102K1
chr3:45781107p.D493N1
chr3:45746631p.I110I1
chr3:45773624p.P512H1
chr3:45785048p.V125V1
chr3:45746689p.A523V1

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 SACM1L 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 SACM1L

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

ACTR8,APPL1,AZI2,FAM208A,CLASP2,DCP1A,DENND6A,
KIAA1143,LZTFL1,NEK4,PBRM1,PDCD6IP,PDE12,QRICH1,
SACM1L,SETD2,SLMAP,TMF1,VPRBP,ZNF197,ZNF621
AP3M1,CDC73,DCUN1D4,ERI1,EXOC1,FAM172A,GDAP2,
GNAQ,LUZP6,NAB1,OSBPL8,SACM1L,SLC30A5,SMAD2,
SMEK2,TBC1D23,TMEM167A,TMX3,USP33,VAMP4,VPS41

TCAIM,C3orf38,TRAPPC13,CAPN7,CRBN,DPH3,EIF1B,
HIGD1A,LYRM7,LZTFL1,MKRN2,OXNAD1,PCNP,PDCD10,
PDHB,RPP14,SACM1L,SELT,SPCS1,UBA3,ZCCHC10
ARFIP1,SMIM15,CAAP1,CD46,MICU2,FPGT,GMFB,
KRCC1,LYSMD3,NRAS,PEX13,RFWD2,SACM1L,SFT2D1,
SGK3,SLMO2,SNX14,TMED5,TMEM167A,VTA1,ZCCHC10
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 SACM1L


There's no related Drug.
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Cross referenced IDs for SACM1L
* 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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