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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for MMAB |
Basic gene info. | Gene symbol | MMAB |
Gene name | methylmalonic aciduria (cobalamin deficiency) cblB type | |
Synonyms | ATR|CFAP23|cblB|cob | |
Cytomap | UCSC genome browser: 12q24 | |
Genomic location | chr12 :109991520-110011358 | |
Type of gene | protein-coding | |
RefGenes | NM_052845.3, NR_038118.1, | |
Ensembl id | ENSG00000139428 | |
Description | ATP:cob(I)alamin adenosyltransferaseATP:corrinoid adenosyltransferaseaquocob(I)alamin vitamin B12s adenosyltransferasecilia and flagella associated protein 23cob(I)yrinic acid a,c-diamide adenosyltransferase, mitochondrialmethylmalonic aciduria type | |
Modification date | 20141219 | |
dbXrefs | MIM : 607568 | |
HGNC : HGNC | ||
Ensembl : ENSG00000139428 | ||
HPRD : 07398 | ||
Vega : OTTHUMG00000169255 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_MMAB | |
BioGPS: 326625 | ||
Gene Expression Atlas: ENSG00000139428 | ||
The Human Protein Atlas: ENSG00000139428 | ||
Pathway | NCI Pathway Interaction Database: MMAB | |
KEGG: MMAB | ||
REACTOME: MMAB | ||
ConsensusPathDB | ||
Pathway Commons: MMAB | ||
Metabolism | MetaCyc: MMAB | |
HUMANCyc: MMAB | ||
Regulation | Ensembl's Regulation: ENSG00000139428 | |
miRBase: chr12 :109,991,520-110,011,358 | ||
TargetScan: NM_052845 | ||
cisRED: ENSG00000139428 | ||
Context | iHOP: MMAB | |
cancer metabolism search in PubMed: MMAB | ||
UCL Cancer Institute: MMAB | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for MMAB(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: MMAB |
Familial Cancer Database: MMAB |
* This gene is included in those cancer gene databases. |
. | ||||||||||||||||||||
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_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: MMAB |
MedGen: MMAB (Human Medical Genetics with Condition) | |
ClinVar: MMAB | |
Phenotype | MGI: MMAB (International Mouse Phenotyping Consortium) |
PhenomicDB: MMAB |
Mutations for MMAB |
* 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 | Top |
- 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'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | MMAB | chr12 | 110005358 | 110005378 | MMAB | chr12 | 110001311 | 110001331 |
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 MMAB 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 |
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=21) | (# total SNVs=5) |
(# 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 |
chr12:110011229-110011229 | p.R19R | 3 |
chr12:110011230-110011230 | p.R19H | 3 |
chr12:110006627-110006627 | p.D80N | 3 |
chr12:109994930-109994930 | p.Y219C | 3 |
chr12:109998867-109998867 | p.V188M | 2 |
chr12:109994870-109994870 | p.M239K | 2 |
chr12:109999595-109999595 | p.E137E | 2 |
chr12:110009504-110009504 | p.S49F | 2 |
chr12:109996961-109996961 | p.? | 1 |
chr12:109999611-109999611 | p.C132S | 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 | 1 | 1 | 3 | 1 |   |   |   | 1 |   |   | 2 |   |   |   |   | 2 | 2 |   | 2 |
# mutation | 1 | 1 | 1 | 3 | 1 |   |   |   | 1 |   |   | 2 |   |   |   |   | 2 | 2 |   | 2 |
nonsynonymous SNV |   |   | 1 | 3 | 1 |   |   |   | 1 |   |   | 2 |   |   |   |   | 2 | 1 |   | 2 |
synonymous SNV | 1 | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | 1 |   |   |
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 |
chr12:110002938 | p.E112K | 2 |
chr12:109998860 | p.R190H | 2 |
chr12:109998890 | p.C132S | 1 |
chr12:109998898 | p.K106K | 1 |
chr12:109999605 | p.E91K | 1 |
chr12:109999611 | p.G87E | 1 |
chr12:109994869 | p.R75S | 1 |
chr12:110002954 | p.S49Y | 1 |
chr12:109994891 | p.M239I | 1 |
chr12:110006594 | p.G232V | 1 |
Other DBs for Point Mutations |
Copy Number for MMAB 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 MMAB |
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 |
COX14,UQCC2,DCXR,DHRS4,DHRS4L2,DPM2,EDF1, ENDOG,LENG9,MMAB,MRPL28,MRPL41,MVK,PHPT1, PSMD9,SDSL,SURF1,TIMM13,TMEM141,TMEM160,UFSP1 | AACS,ACAT2,ACY1,BCAT2,URB1-AS1,DBI,DCXR, DHCR7,EBP,FDPS,GSS,GSTZ1,HIST1H1C,HIST2H2AA3, IVD,MMAB,MVD,MVK,NSDHL,PEX10,REEP6 | ||||
ARL6IP4,CDK4,COX6A1,DIABLO,EBP,METTL1,MMAB, MVK,NDUFA12,NOC4L,NUP37,NABP2,PA2G4,RAN, RPLP0,SRSF9,SLC25A3,SNRPF,TARBP2,TSFM,TUBA1C | BOLA3,HYPK,EBNA1BP2,EIF3I,EIF5A,EIF5AL1,HSD17B7, MMAB,MRPL17,MRPL20,MRPL52,NHP2,NME1,PPIL1, PSMA7,PSMD14,RAN,RFC2,SNRPG,TMSB10,TOMM5 |
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 MMAB |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00200 | methylmalonic aciduria (cobalamin deficiency) cblB type | approved | Hydroxocobalamin |
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Cross referenced IDs for MMAB |
* 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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