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 SEC24D
Basic gene info.Gene symbolSEC24D
Gene nameSEC24 family member D
Synonyms-
CytomapUCSC genome browser: 4q26
Genomic locationchr4 :119643977-119757326
Type of geneprotein-coding
RefGenesNM_014822.2,
Ensembl idENSG00000150961
DescriptionSEC24 family, member DSEC24 related gene family, member DSEC24-related protein Dprotein transport protein Sec24D
Modification date20141207
dbXrefs MIM : 607186
HGNC : HGNC
Ensembl : ENSG00000150961
HPRD : 06218
Vega : OTTHUMG00000132957
ProteinUniProt: O94855
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SEC24D
BioGPS: 9871
Gene Expression Atlas: ENSG00000150961
The Human Protein Atlas: ENSG00000150961
PathwayNCI Pathway Interaction Database: SEC24D
KEGG: SEC24D
REACTOME: SEC24D
ConsensusPathDB
Pathway Commons: SEC24D
MetabolismMetaCyc: SEC24D
HUMANCyc: SEC24D
RegulationEnsembl's Regulation: ENSG00000150961
miRBase: chr4 :119,643,977-119,757,326
TargetScan: NM_014822
cisRED: ENSG00000150961
ContextiHOP: SEC24D
cancer metabolism search in PubMed: SEC24D
UCL Cancer Institute: SEC24D
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for SEC24D(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SEC24D
Familial Cancer Database: SEC24D
* 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 607186; gene.
Orphanet
DiseaseKEGG Disease: SEC24D
MedGen: SEC24D (Human Medical Genetics with Condition)
ClinVar: SEC24D
PhenotypeMGI: SEC24D (International Mouse Phenotyping Consortium)
PhenomicDB: SEC24D

Mutations for SEC24D
* 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
ovarySEC24Dchr4119661379119661399chr4118671938118671958
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 SEC24D related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE695910SEC24D192634119643989119644235TPM32546361154158571154158956
BE695881TPM3313411154158571154158880SEC24D3324944119644073119644235
AW853022TPM394041154158571154158968SEC24D3956324119643998119644235
BE695897SEC24D332794119643989119644235TPM32706591154158571154158962
BE695898SEC24D362804119643989119644235TPM32716681154158571154158968

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 # sample1                
GAIN (# sample)1                
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)

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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=80)
Stat. for Synonymous SNVs
(# total SNVs=16)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr4:119660425-119660425p.T752T3
chr4:119678939-119678939p.I453K3
chr4:119653922-119653922p.S881C2
chr4:119736796-119736796p.P161P2
chr4:119644736-119644736p.Y1011Y2
chr4:119660412-119660412p.Q757*2
chr4:119674014-119674014p.R484L2
chr4:119685980-119685980p.V425L2
chr4:119686021-119686021p.H411L2
chr4:119654014-119654014p.L850L2

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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
# sample24211  3 1  83  1127216
# mutation24215  3 1  83  11310221
nonsynonymous SNV 4213  2 1  62   107118
synonymous SNV2  2  1    21  13313
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
chr4:119754819p.P11P3
chr4:119736623p.G219V2
chr4:119644736p.Y1011Y2
chr4:119660425p.T752T2
chr4:119653922p.R907C2
chr4:119652620p.S881F2
chr4:119665262p.A830T1
chr4:119736304p.V626M1
chr4:119644689p.P437H1
chr4:119652625p.S227C1

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 SEC24D 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 SEC24D

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

COPB1,DNAJB14,G3BP2,IBTK,IDE,KIAA1033,MAP3K2,
METTL14,PRRC1,SEC24A,SEC24B,SEC24D,SEC31A,SETD7,
SETX,SLC10A7,TMED7-TICAM2,TNPO1,USO1,USP38,YIPF5
ACTR3,PARPBP,CDC7,DCAF12,DNAJC10,E2F3,ECT2,
EIF2AK3,F2R,KPNA2,LHFPL2,MXRA5,NRAS,PTGFRN,
PTPN9,SEC24D,SLC30A7,SLC39A10,UBTD2,VASH2,ZWILCH

AGR2,ARFGAP3,TMEM263,EDEM1,ENTPD7,FAM114A1,TVP23B,
FAM46A,FUT11,HIF1A,IKBIP,KDELR3,MAPRE2,NDEL1,
NUCB2,PDLIM5,PRRC1,RAB27A,SEC24A,SEC24D,SLC30A7
AGR2,AP1S3,ARCN1,ARFGAP3,TMEM263,CGREF1,COG5,
GLYATL1,GOSR2,KDELR3,P4HB,PGM3,PRSS22,REG4,
S100P,SEC13,SEC22B,SEC24D,SLC6A14,TSPO2,TSTA3
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 SEC24D


There's no related Drug.
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Cross referenced IDs for SEC24D
* 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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