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 SUMF1
Basic gene info.Gene symbolSUMF1
Gene namesulfatase modifying factor 1
SynonymsAAPA3037|FGE
CytomapUCSC genome browser: 3p26.1
Genomic locationchr3 :4402828-4508966
Type of geneprotein-coding
RefGenesNM_001164674.1,
NM_001164675.1,NM_182760.3,
Ensembl idENSG00000144455
DescriptionC-alpha-formylglycine-generating enzyme 1FGly-generating enzymesulfatase-modifying factor 1
Modification date20141207
dbXrefs MIM : 607939
HGNC : HGNC
Ensembl : ENSG00000144455
HPRD : 06399
Vega : OTTHUMG00000090269
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SUMF1
BioGPS: 285362
Gene Expression Atlas: ENSG00000144455
The Human Protein Atlas: ENSG00000144455
PathwayNCI Pathway Interaction Database: SUMF1
KEGG: SUMF1
REACTOME: SUMF1
ConsensusPathDB
Pathway Commons: SUMF1
MetabolismMetaCyc: SUMF1
HUMANCyc: SUMF1
RegulationEnsembl's Regulation: ENSG00000144455
miRBase: chr3 :4,402,828-4,508,966
TargetScan: NM_001164674
cisRED: ENSG00000144455
ContextiHOP: SUMF1
cancer metabolism search in PubMed: SUMF1
UCL Cancer Institute: SUMF1
Assigned class in ccmGDBC

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Phenotypic Information for SUMF1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SUMF1
Familial Cancer Database: SUMF1
* 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_GLYCOSPHINGOLIPID_METABOLISM
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_METABOLISM_OF_PROTEINS
REACTOME_SPHINGOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SUMF1
MedGen: SUMF1 (Human Medical Genetics with Condition)
ClinVar: SUMF1
PhenotypeMGI: SUMF1 (International Mouse Phenotyping Consortium)
PhenomicDB: SUMF1

Mutations for SUMF1
* 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
pancreasSUMF1chr344244044424424chr343927214392741
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 SUMF1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
XX000010SUMF1151344180134418063LRRFIP25012533717056637170641
AW236721SUMF12141344028354402974PRPF38B1383771109241803109242042
AI127082SUMF1676344028314402901SUMF175297344029524403174
BE831647SMAD77135184644804546448175SUMF1129383338414943886191
AI126937SUMF1171344028314402901SUMF170292344029524403174

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 # sample5     1          
GAIN (# sample)3                
LOSS (# sample)2     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=23)		Stat. for Synonymous SNVs
(# total SNVs=7)
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
chr3:4508742-4508742p.S63N6
chr3:4403829-4403829p.*375*2
chr3:4403837-4403837p.T372T2
chr3:4508800-4508800p.G44R2
chr3:4403869-4403869p.G362R2
chr3:4418033-4418033p.G332E2
chr3:4459798-4459798p.L207L2
chr3:4494730-4494730p.V92F1
chr3:4452578-4452578p.H309Y1
chr3:4461752-4461752p.H200Y1

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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
# sample1 12  2  1 51    5 6
# mutation1 12  2  1 51    4 6
nonsynonymous SNV1 12  2  1 4     3 4
synonymous SNV           11    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
chr3:4452611p.A273T,SUMF12
chr3:4458925p.V166G,SUMF11
chr3:4494692p.D154N,SUMF11
chr3:4459714p.R344H,SUMF11
chr3:4494724p.G153G,SUMF11
chr3:4403847p.A322T,SUMF11
chr3:4459759p.S132S,SUMF11
chr3:4494730p.R313M,SUMF11
chr3:4403914p.A116E,SUMF11
chr3:4461752p.M310T,SUMF11

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 SUMF1 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 SUMF1

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

ACOT4,ALG1,ARL8B,BCDIN3D,BTD,CCDC103,COQ7,
EARS2,FAM134A,FAM134C,G6PC3,HMGCL,HSD17B8,ZNF205-AS1,
ORAI3,PIGV,RBKS,SUMF1,TMBIM6,TMEM9B,TTC39A		CHTF8,CLPTM1L,CYB5D2,GBA,LAMP1,LHPP,MFSD5,
ORMDL2,PDZD11,POLR2G,PPCS,RPN1,SCAMP2,SUMF1,
TM2D2,TM9SF1,TMEM127,TOR1A,TRAPPC3,TSPAN31,UFC1

BTD,C11orf71,PPP1R36,TCAIM,CMTM6,ESRP1,FXYD3,
GLT8D1,GPRC5C,HMGCL,LOC100128640,PIGP,PIGV,SAMD13,
SUMF1,TADA3,TEX264,TMEM115,TMEM134,TMEM141,TMEM42		ADCK2,PROSER2,TMEM246,C9orf152,CWH43,FOXA1,FOXD2,
FRAT2,IMPA2,KREMEN1,LRRC31,MAZ,MTL5,MYCL,
PABPC1,PPP1R1B,QARS,SFT2D3,SMAGP,SUMF1,TMEM44
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 SUMF1


There's no related Drug.
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Cross referenced IDs for SUMF1
* 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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