Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 SMN1

Basic gene info.	Gene symbol	SMN1
	Gene name	survival of motor neuron 1, telomeric
	Synonyms	BCD541\|GEMIN1\|SMA\|SMA1\|SMA2\|SMA3\|SMA4\|SMA@\|SMN\|SMNT\|T-BCD541\|TDRD16A
	Cytomap	UCSC genome browser: 5q13.2
	Genomic location	chr5 :70220767-70248838
	Type of gene	protein-coding
	RefGenes	NM_000344.3, NM_001297715.1,NM_022874.2,
	Ensembl id	ENSG00000172062
	Description	component of gems 1gemin-1survival motor neuron 1 proteinsurvival motor neuron proteintudor domain containing 16A
	Modification date	20141219
dbXrefs	MIM : 600354
	HGNC : HGNC
	Ensembl : ENSG00000172062
	HPRD : 02646
	Vega : OTTHUMG00000099361
Protein	UniProt: Q16637 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SMN1
	BioGPS: 6606
	Gene Expression Atlas: ENSG00000172062
	The Human Protein Atlas: ENSG00000172062
Pathway	NCI Pathway Interaction Database: SMN1
	KEGG: SMN1
	REACTOME: SMN1
	ConsensusPathDB
	Pathway Commons: SMN1
Metabolism	MetaCyc: SMN1
	HUMANCyc: SMN1
Regulation	Ensembl's Regulation: ENSG00000172062
	miRBase: chr5 :70,220,767-70,248,838
	TargetScan: NM_000344
	cisRED: ENSG00000172062
Context	iHOP: SMN1
	cancer metabolism search in PubMed: SMN1
	UCL Cancer Institute: SMN1
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for SMN1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SMN1
	Familial Cancer Database: SMN1

* 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_NON_CODING_RNA REACTOME_METABOLISM_OF_RNA

Others
OMIM	253300; phenotype. 253400; phenotype. 253550; phenotype. 271150; phenotype. 600354; gene. 601627; gene.
Orphanet	83330; Proximal spinal muscular atrophy type 1. 83418; Proximal spinal muscular atrophy type 2. 83419; Proximal spinal muscular atrophy type 3. 83420; Proximal spinal muscular atrophy type 4.
Disease	KEGG Disease: SMN1
	MedGen: SMN1 (Human Medical Genetics with Condition)
	ClinVar: SMN1
Phenotype	MGI: SMN1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SMN1

Mutations for SMN1

* 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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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

There's no intra-chromosomal structural variation.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	SMN1	chr5	70241400	70241420	LINC00536	chr8	117234746	117234766

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SMN1 related fusion information.

Head Gene

Tail Gene

Accession

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy 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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SNV 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=1

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=0)	Stat. for Synonymous SNVs (# total SNVs=1)
There's no ns-snv.
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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Top 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 position	Mutation(aa)	Unique sampleID count
chr5:70241907-70241907	p.P246P	1

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SNV Counts per Each Loci in TCGA data

: non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=0

Point Mutation/ Tissue ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample
# mutation
nonsynonymous SNV
synonymous SNV

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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Top 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 Position

Mutation(aa)

Unique sampleID count

Other 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

Copy Number for SMN1 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 SMN1

Gene 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.

Differential 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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CNV 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

Co-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


AGGF1,ATG12,SMIM15,CETN3,COMMD10,GPBP1,MIER3, MRPS36,POC5,RAD17,RRN3,SCAMP1,SERF1A,SREK1IP1, SRSF1,SMN1,SMN2,TAF9,ZCCHC8,ZCCHC9,ZFYVE16	CHPT1,CYLC2,DIMT1,EEF1E1,GPR89B,HCRT,IER3IP1, LOC286094,LSM5,PNRC1,PPP1R8,PRSS38,PRSS41,RSL24D1, RWDD4,SMN1,SPCS2,TMEM9B,TPRKB,WTAP,ZNF639

CCNH,CENPK,METTL21A,GPR149,MFF,NIF3L1,NUP35, OR10J1,ORM2,RBM44,SRSF7,SLC39A12,SMN1,SMN2, SUMO1P3,TAF9,TBCA,UBE2D2,ZC3H15,ZCCHC9,ZNF207	C17orf97,TMEM246,CABP2,CGB8,CIB3,DEFB119,ENDOG, HGC6.3,HIGD2A,ID3,LOC284379,OR10G9,OR52L1,PDHA2, SCARNA21,SCGB1D1,SERF1A,SMN1,SNORA77,TBR1,VENTXP7

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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 SMN1

There's no related Drug.

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Cross referenced IDs for SMN1

* 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