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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for MLYCD |
Basic gene info. | Gene symbol | MLYCD |
Gene name | malonyl-CoA decarboxylase | |
Synonyms | MCD | |
Cytomap | UCSC genome browser: 16q24 | |
Genomic location | chr16 :83932729-83949787 | |
Type of gene | protein-coding | |
RefGenes | NM_012213.2, | |
Ensembl id | ENSG00000103150 | |
Description | malonyl coenzyme A decarboxylasemalonyl-CoA decarboxylase, mitochondrial | |
Modification date | 20141207 | |
dbXrefs | MIM : 606761 | |
HGNC : HGNC | ||
HPRD : 05999 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_MLYCD | |
BioGPS: 23417 | ||
Gene Expression Atlas: ENSG00000103150 | ||
The Human Protein Atlas: ENSG00000103150 | ||
Pathway | NCI Pathway Interaction Database: MLYCD | |
KEGG: MLYCD | ||
REACTOME: MLYCD | ||
ConsensusPathDB | ||
Pathway Commons: MLYCD | ||
Metabolism | MetaCyc: MLYCD | |
HUMANCyc: MLYCD | ||
Regulation | Ensembl's Regulation: ENSG00000103150 | |
miRBase: chr16 :83,932,729-83,949,787 | ||
TargetScan: NM_012213 | ||
cisRED: ENSG00000103150 | ||
Context | iHOP: MLYCD | |
cancer metabolism search in PubMed: MLYCD | ||
UCL Cancer Institute: MLYCD | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for MLYCD(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: MLYCD |
Familial Cancer Database: MLYCD |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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 | |
KEGG_BETA_ALANINE_METABOLISM KEGG_PROPANOATE_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: MLYCD |
MedGen: MLYCD (Human Medical Genetics with Condition) | |
ClinVar: MLYCD | |
Phenotype | MGI: MLYCD (International Mouse Phenotyping Consortium) |
PhenomicDB: MLYCD |
Mutations for MLYCD |
* 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 MLYCD 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 |
BF805316 | MLYCD | 1 | 123 | 16 | 83935396 | 83935519 | MLYCD | 119 | 308 | 16 | 83935205 | 83935394 |
Other DBs for Structural Variants |
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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 |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=28) | (# total SNVs=11) |
(# total SNVs=0) | (# total SNVs=0) |
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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 |
chr16:83940603-83940603 | p.G180G | 2 |
chr16:83948787-83948787 | p.R392L | 2 |
chr16:83948976-83948976 | p.R455H | 1 |
chr16:83941865-83941865 | p.G259A | 1 |
chr16:83948559-83948560 | p.? | 1 |
chr16:83948790-83948790 | p.A393V | 1 |
chr16:83940609-83940609 | p.L182L | 1 |
chr16:83949024-83949024 | p.S471F | 1 |
chr16:83945829-83945829 | p.V269M | 1 |
chr16:83948685-83948685 | p.S358L | 1 |
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SNV Counts per Each Loci in TCGA data |
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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 | 1 | 2 |   |   | 1 |   |   |   | 3 |   |   | 2 | 1 |   | 1 |   | 3 | 6 |   | 5 |
# mutation | 1 | 2 |   |   | 1 |   |   |   | 3 |   |   | 3 | 1 |   | 1 |   | 4 | 6 |   | 5 |
nonsynonymous SNV |   | 1 |   |   | 1 |   |   |   | 2 |   |   | 3 | 1 |   |   |   | 3 | 5 |   | 3 |
synonymous SNV | 1 | 1 |   |   |   |   |   |   | 1 |   |   |   |   |   | 1 |   | 1 | 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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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 |
chr16:83948758 | p.A286V | 2 |
chr16:83945881 | p.S382S | 2 |
chr16:83948728 | p.S447S | 1 |
chr16:83949048 | p.R199L | 1 |
chr16:83940640 | p.C448C | 1 |
chr16:83948731 | p.E214D | 1 |
chr16:83940659 | p.R455H | 1 |
chr16:83941731 | p.T245A | 1 |
chr16:83948828 | p.S471F | 1 |
chr16:83933047 | p.Q479R | 1 |
Other DBs for Point Mutations |
Copy Number for MLYCD 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 MLYCD |
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. |
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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 |
ACSF3,ATP6V0D1,CES2,CHMP1A,COG4,COG8,EDC4, ELMO3,FBXO31,FUK,GABARAPL2,GAS8,KATNB1,IST1, MBTPS1,MLYCD,PRMT7,PSKH1,SPG7,TCF25,VPS4A | ACAT1,ACO2,ALPK3,ATP1A2,ATP5B,ADCK3,CHCHD10, CHCHD3,COX5A,GYS1,IMMT,MLYCD,OGDH,RAD23A, RXRG,SCN4A,SDHA,SDHB,SIRT2,SNTA1,UQCRFS1 |
ACSF3,ALG1,ATP6V0D1,CHMP1A,CLN3,COG4,COQ9, EDC4,ESRP2,FBXO31,FUK,MBTPS1,MLYCD,MON1B, PSKH1,SPG7,TCF25,TERF2,USP10,VPS4A,WWP2 | ADH1C,ATPAF2,BDH1,C21orf33,GJB1,GSS,MCCC1, MEST,MLYCD,MRPS30,MRPS5,NDUFA10,NDUFV1,PCCA, PIGU,PNPO,STARD7,SUPV3L1,TBRG4,THNSL1,UNG |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for MLYCD |
There's no related Drug. |
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Cross referenced IDs for MLYCD |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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