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

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 SEC61A1

Basic gene info.	Gene symbol	SEC61A1
	Gene name	Sec61 alpha 1 subunit (S. cerevisiae)
	Synonyms	HSEC61\|SEC61\|SEC61A
	Cytomap	UCSC genome browser: 3q21.3
	Genomic location	chr3 :127771211-127790526
	Type of gene	protein-coding
	RefGenes	NM_013336.3,
	Ensembl id	ENSG00000058262
	Description	Sec61 alpha-1protein transport protein SEC61 alpha subunitprotein transport protein Sec61 subunit alphaprotein transport protein Sec61 subunit alpha isoform 1sec61 homolog
	Modification date	20141207
dbXrefs	MIM : 609213
	HGNC : HGNC
	Ensembl : ENSG00000058262
	HPRD : 15316
	Vega : OTTHUMG00000159624
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SEC61A1
	BioGPS: 29927
	Gene Expression Atlas: ENSG00000058262
	The Human Protein Atlas: ENSG00000058262
Pathway	NCI Pathway Interaction Database: SEC61A1
	KEGG: SEC61A1
	REACTOME: SEC61A1
	ConsensusPathDB
	Pathway Commons: SEC61A1
Metabolism	MetaCyc: SEC61A1
	HUMANCyc: SEC61A1
Regulation	Ensembl's Regulation: ENSG00000058262
	miRBase: chr3 :127,771,211-127,790,526
	TargetScan: NM_013336
	cisRED: ENSG00000058262
Context	iHOP: SEC61A1
	cancer metabolism search in PubMed: SEC61A1
	UCL Cancer Institute: SEC61A1
Assigned class in ccmGDB	C

Top

Phenotypic Information for SEC61A1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SEC61A1
	Familial Cancer Database: SEC61A1

* 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_PROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: SEC61A1
	MedGen: SEC61A1 (Human Medical Genetics with Condition)
	ClinVar: SEC61A1
Phenotype	MGI: SEC61A1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SEC61A1

Mutations for SEC61A1

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SEC61A1 related fusion information.

ID	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
BF959743	DIDO1	14	368	20	61538603	61541296	SEC61A1	360	431	3	127789080	127789151
AW105324	SEC61A1	1	193	3	127790242	127790434	CCT5	190	315	5	10262662	10263302
DA769011	SNHG1	1	66	11	62622486	62622551	SEC61A1	66	518	3	127785924	127788431
DA580258	ZC3H11A	1	155	1	203764776	203764930	SEC61A1	156	562	3	127775637	127783815
AA405428	SEC61A1	41	149	3	127787546	127787654	SEC61A1	144	392	3	127788221	127788468
AW939919	SEC61A1	1	136	3	127789016	127789152	SEC61A1	119	223	3	127789165	127789271
AW897979	GUCY1A3	12	488	4	156653270	156653746	SEC61A1	478	636	3	127788885	127789044
BE835544	UBTF	1	278	17	42285808	42286084	SEC61A1	275	432	3	127789422	127789579
BF748943	SEC61A1	16	253	3	127789430	127789668	SEC61A1	247	596	3	127788923	127789272

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

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)

Top

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=4

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=33)	Stat. for Synonymous SNVs (# total SNVs=5)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	There's no inserted snv.

Top

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
chr3:127788458-127788458	p.V462I	2
chr3:127783746-127783746	p.A215T	2
chr3:127786902-127786902	p.R415L	2
chr3:127783771-127783771	p.R223H	2
chr3:127779411-127779411	p.L175I	2
chr3:127783794-127783794	p.R231W	2
chr3:127783795-127783795	p.R231Q	2
chr3:127785825-127785825	p.S269L	2
chr3:127775570-127775570	p.G80E	1
chr3:127786443-127786443	p.S385S	1

Top

SNV Counts per Each Loci in TCGA data

: non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=3

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		2		9			3		1			4	2	2		1	3	5		4
# mutation		2		8			3		1			5	2	2		1	3	6		4
nonsynonymous SNV		2		8			2					4	2	2		1	1	2		4
synonymous SNV							1		1			1					2	4

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])

Top

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
chr3:127783746	p.A215T	3
chr3:127785825	p.R415Q	2
chr3:127786902	p.R231L	2
chr3:127788458	p.S269L	2
chr3:127783795	p.V462I	2
chr3:127775657	p.T286T	1
chr3:127783841	p.G80E	1
chr3:127786843	p.Y302Y	1
chr3:127778995	p.T105A	1
chr3:127786876	p.V303V	1

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 SEC61A1 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]

Top

Gene Expression for SEC61A1

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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

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


ACAD9,AP2M1,TIMMDC1,HMCES,CALR,COPB2,COPG1, DDOST,DNAJB11,HSP90B1,HYOU1,ISY1,P4HB,PDIA4, PDIA5,PDIA6,RPN1,SEC61A1,SRPRB,TMEM214,TMEM39A	AP1B1,CALR,CHPF2,CHPF,CKAP4,CNDP2,DDOST, GMPPB,HSPA5,HYOU1,P4HB,PDIA3P1,PDIA4,PDIA6, RPN1,RUVBL1,SEC61A1,SEPT9,SRPRB,ST14,YARS

CKAP4,COPB2,COPG1,DNAJC3,EIF4G1,GLG1,GMPPA, HDLBP,HSPA5,HYOU1,NUCB2,P4HB,PDIA5,RPN1, SEC24D,SEC61A1,SLC39A7,SSR3,SURF4,TMED9,TMEM214	COPG1,EFTUD2,HIRA,HNRNPM,HYOU1,LMNB2,LOC401010, MED24,MTA2,MYO1B,NCLN,PDIA4,PTBP1,RPN2, SEC61A1,SLC5A6,STT3A,TMEM104,TMEM214,UGGT1,VARS

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

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for SEC61A1

There's no related Drug.

Top

Cross referenced IDs for SEC61A1

* 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