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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for CDA |
Basic gene info. | Gene symbol | CDA |
Gene name | cytidine deaminase | |
Synonyms | CDD | |
Cytomap | UCSC genome browser: 1p36.2-p35 | |
Genomic location | chr1 :20915443-20945400 | |
Type of gene | protein-coding | |
RefGenes | NM_001785.2, | |
Ensembl id | ENSG00000158825 | |
Description | cytidine aminohydrolasecytosine nucleoside deaminasesmall cytidine deaminase | |
Modification date | 20141222 | |
dbXrefs | MIM : 123920 | |
HGNC : HGNC | ||
Ensembl : ENSG00000158825 | ||
HPRD : 11744 | ||
Vega : OTTHUMG00000002845 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_CDA | |
BioGPS: 978 | ||
Gene Expression Atlas: ENSG00000158825 | ||
The Human Protein Atlas: ENSG00000158825 | ||
Pathway | NCI Pathway Interaction Database: CDA | |
KEGG: CDA | ||
REACTOME: CDA | ||
ConsensusPathDB | ||
Pathway Commons: CDA | ||
Metabolism | MetaCyc: CDA | |
HUMANCyc: CDA | ||
Regulation | Ensembl's Regulation: ENSG00000158825 | |
miRBase: chr1 :20,915,443-20,945,400 | ||
TargetScan: NM_001785 | ||
cisRED: ENSG00000158825 | ||
Context | iHOP: CDA | |
cancer metabolism search in PubMed: CDA | ||
UCL Cancer Institute: CDA | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for CDA(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: CDA |
Familial Cancer Database: CDA |
* 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_PYRIMIDINE_METABOLISM KEGG_DRUG_METABOLISM_OTHER_ENZYMES REACTOME_METABOLISM_OF_NUCLEOTIDES REACTOME_PYRIMIDINE_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: CDA |
MedGen: CDA (Human Medical Genetics with Condition) | |
ClinVar: CDA | |
Phenotype | MGI: CDA (International Mouse Phenotyping Consortium) |
PhenomicDB: CDA |
Mutations for CDA |
* 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 CDA 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 |
BM850111 | NEDD8-MDP1 | 1 | 512 | 14 | 24686165 | 24701571 | CDA | 507 | 570 | 1 | 20945065 | 20945128 | |
BU634160 | CDA | 40 | 218 | 1 | 20923871 | 21310549 | GNPTAB | 213 | 718 | 12 | 102140628 | 102147173 | |
BF901504 | CCHCR1 | 1 | 367 | 6 | 2409347 | 2413749 | CDA | 368 | 461 | 1 | 20938233 | 20938325 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample |   | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
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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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=19) | (# total SNVs=3) |
(# total SNVs=0) | (# total SNVs=1) |
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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 |
chr1:20931489-20931489 | p.V75I | 2 |
chr1:20931490-20931490 | p.V75A | 2 |
chr1:20945033-20945033 | p.G138E | 2 |
chr1:20915701-20915701 | p.K27Q | 2 |
chr1:20931527-20931527 | p.I87I | 2 |
chr1:20931468-20931468 | p.R68W | 1 |
chr1:20944945-20944945 | p.F109V | 1 |
chr1:20931469-20931469 | p.R68L | 1 |
chr1:20944968-20944968 | p.Y116Y | 1 |
chr1:20915650-20915650 | p.L10V | 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 |   |   | 3 | 3 |   |   |   |   |   |   | 1 | 1 | 1 |   |   | 3 | 1 |   | 2 |
# mutation | 1 |   |   | 2 | 3 |   |   |   |   |   |   | 1 | 1 | 1 |   |   | 4 | 1 |   | 2 |
nonsynonymous SNV |   |   |   | 2 | 2 |   |   |   |   |   |   |   | 1 | 1 |   |   | 1 | 1 |   | 2 |
synonymous SNV | 1 |   |   |   | 1 |   |   |   |   |   |   | 1 |   |   |   |   | 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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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 |
chr1:20931490 | p.V75A | 2 |
chr1:20931527 | p.T123A | 1 |
chr1:20931528 | p.G138E | 1 |
chr1:20915652 | p.L10L | 1 |
chr1:20944968 | p.L18L | 1 |
chr1:20915674 | p.F50F | 1 |
chr1:20944973 | p.P61Q | 1 |
chr1:20915772 | p.V75I | 1 |
chr1:20944980 | p.G78E | 1 |
chr1:20931448 | p.K80N | 1 |
Other DBs for Point Mutations |
Copy Number for CDA 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 CDA |
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 |
CALB1,CCL24,CDA,COL7A1,CSF2,DEFB103B,IFNK, IL1A,KRT14,KRT6A,KRT6C,KRTAP11-1,LAMC2,SFN, SPINK7,SPRR1B,TMPRSS11D,TRIML2,UCN2,WNT7A,ZBED2 | C1QTNF2,C1QTNF3,CD70,CDA,CLEC10A,DNM1,EMP3, FBN1,FOLR2,FSTL1,GFPT2,GPR133,HRH1,HTRA3, LGI2,LMX1A,MFAP5,PROCR,SPSB4,WNT10B,XPNPEP2 | ||||
LINC00520,C16orf74,CDA,DHRS9,ELOVL1,EMP1,FAM25A, FAM25BP,GJB3,GJB4,KLK8,KRT19,LAMA3,LAMB3, LOC100216001,PLIN3,POLD4,PXN,RHOD,RHOF,SLC2A1 | C11orf86,C1orf177,CDA,CLCA4,CLTB,DIRC2,GUCA2A, HIST1H1C,KRT8,PLA2G2F,PLIN3,POLD4,RHBDF1,RHOC, RHOG,SAMD9,SH3BGRL3,SIRT6,TSPAN1,UNC13D,ZNF622 |
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 CDA |
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 |
DB00987 | cytidine deaminase | approved; investigational | Cytarabine | ||
DB01101 | cytidine deaminase | approved; investigational | Capecitabine | ||
DB00544 | cytidine deaminase | approved | Fluorouracil | ||
DB02745 | cytidine deaminase | experimental | Uridine | ||
DB00928 | cytidine deaminase | approved; investigational | Azacitidine | ||
DB00313 | cytidine deaminase | approved; investigational | Valproic Acid | ||
DB00441 | cytidine deaminase | approved | Gemcitabine | ||
DB00515 | cytidine deaminase | approved | Cisplatin |
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Cross referenced IDs for CDA |
* 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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