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 SEC24B
Basic gene info.Gene symbolSEC24B
Gene nameSEC24 family member B
SynonymsSEC24
CytomapUCSC genome browser: 4q25
Genomic locationchr4 :110354970-110461615
Type of geneprotein-coding
RefGenesNM_001042734.2,
NM_001300813.1,NM_006323.3,
Ensembl idENSG00000138802
DescriptionSEC24 related gene family, member Bprotein transport protein Sec24Bsecretory protein 24
Modification date20141207
dbXrefs MIM : 607184
HGNC : HGNC
Ensembl : ENSG00000138802
HPRD : 06216
Vega : OTTHUMG00000161372
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SEC24B
BioGPS: 10427
Gene Expression Atlas: ENSG00000138802
The Human Protein Atlas: ENSG00000138802
PathwayNCI Pathway Interaction Database: SEC24B
KEGG: SEC24B
REACTOME: SEC24B
ConsensusPathDB
Pathway Commons: SEC24B
MetabolismMetaCyc: SEC24B
HUMANCyc: SEC24B
RegulationEnsembl's Regulation: ENSG00000138802
miRBase: chr4 :110,354,970-110,461,615
TargetScan: NM_001042734
cisRED: ENSG00000138802
ContextiHOP: SEC24B
cancer metabolism search in PubMed: SEC24B
UCL Cancer Institute: SEC24B
Assigned class in ccmGDBC

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Phenotypic Information for SEC24B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SEC24B
Familial Cancer Database: SEC24B
* 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_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SEC24B
MedGen: SEC24B (Human Medical Genetics with Condition)
ClinVar: SEC24B
PhenotypeMGI: SEC24B (International Mouse Phenotyping Consortium)
PhenomicDB: SEC24B

Mutations for SEC24B
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SEC24B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AV726458SEC24B15304110384093110384622MALAT1526685116527065065270813
AV715572SEC24B14574110450428110450882SEC24B4565604110449940110450044

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

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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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=78)
Stat. for Synonymous SNVs
(# total SNVs=26)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr4:110384109-110384109p.Q62Q3
chr4:110384361-110384361p.T146T3
chr4:110384452-110384453p.P177F2
chr4:110433113-110433113p.Q558*2
chr4:110447419-110447419p.V908V2
chr4:110415930-110415930p.G434D2
chr4:110433153-110433153p.R571Q2
chr4:110442602-110442602p.L741L2
chr4:110451548-110451548p.L1025F2
chr4:110437770-110437770p.C665C2

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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
# sample36 173 5 21 1042 1814 13
# mutation46 163 5 21 1442 1815 14
nonsynonymous SNV23 131 4 21 731 1210 11
synonymous SNV23 42 1    711  65 3
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
chr4:110448544p.Q536H,SEC24B2
chr4:110431204p.R772H,SEC24B2
chr4:110442694p.A976V,SEC24B2
chr4:110384608p.T1054T,SEC24B1
chr4:110427546p.H249Q,SEC24B1
chr4:110445990p.P404S,SEC24B1
chr4:110394218p.R526W,SEC24B1
chr4:110433153p.C665C,SEC24B1
chr4:110415906p.L829V,SEC24B1
chr4:110442579p.T1056K,SEC24B1

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 SEC24B 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 SEC24B

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

BOD1L1,C4orf29,TRAPPC11,CLCN3,CLOCK,DNAJB14,DPP8,
KIAA1109,CFAP97,LIN54,METTL14,REST,RNF111,SEC24B,
SMARCAD1,TET2,TMEM184C,UBE2D3,UBR3,USP38,WDFY3
ARIH1,ATRX,TRAPPC11,CAPN7,COG5,TRAPPC8,KIAA2026,
KRIT1,MORC3,RAB3GAP2,LTN1,RPS6KB1,SEC24B,SCAF11,
SKIV2L2,SP1,STAG2,TAB2,USP8,ZFX,ZNF280D

AFF1,ANKRD17,AP1AR,TRAPPC11,CLCN3,DNAJB14,G3BP2,
HERC3,KIAA1109,LRBA,METTL14,OTUD4,SEC24B,SH3D19,
SMAD1,SMARCA5,TMEM184C,UBE2D3,USP38,USP53,WDFY3
ANKHD1,ARID2,CLTC,CNOT1,CSNK2A1,CTCF,DDX6,
DLG1,GAPVD1,GNAQ,MAPK1,MED13,OSBPL11,PAFAH1B1,
PHF3,RALGAPB,RNF111,SEC24B,SEL1L,SCAF11,USP9X
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 SEC24B


There's no related Drug.
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Cross referenced IDs for SEC24B
* 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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