Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 PISD
Basic gene info.Gene symbolPISD
Gene namephosphatidylserine decarboxylase
SynonymsDJ858B16|PSD|PSDC|PSSC|dJ858B16.2
CytomapUCSC genome browser: 22q12.2
Genomic locationchr22 :32014476-32026810
Type of geneprotein-coding
RefGenesNM_014338.3,
Ensembl idENSG00000241878
Descriptionphosphatidylserine decarboxylase proenzyme
Modification date20141207
dbXrefs MIM : 612770
HGNC : HGNC
Ensembl : ENSG00000241878
HPRD : 17854
Vega : OTTHUMG00000030252
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PISD
BioGPS: 23761
Gene Expression Atlas: ENSG00000241878
The Human Protein Atlas: ENSG00000241878
PathwayNCI Pathway Interaction Database: PISD
KEGG: PISD
REACTOME: PISD
ConsensusPathDB
Pathway Commons: PISD
MetabolismMetaCyc: PISD
HUMANCyc: PISD
RegulationEnsembl's Regulation: ENSG00000241878
miRBase: chr22 :32,014,476-32,026,810
TargetScan: NM_014338
cisRED: ENSG00000241878
ContextiHOP: PISD
cancer metabolism search in PubMed: PISD
UCL Cancer Institute: PISD
Assigned class in ccmGDBC

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

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

Mutations for PISD
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
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 PISD related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF996842RORB935897720955477209904PISD350519223201473132014900
BP321628PISD1511223201495332015463PISD504582223201764532017723
BQ375244PISD1176223201526332015438PISD174278223201544532015549

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample        1    1   
GAIN (# sample)        1    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)

Top
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=5

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=22)
Stat. for Synonymous SNVs
(# total SNVs=12)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

Top
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
chr22:32015676-32015676p.F350F3
chr22:32017668-32017668p.P141P3
chr22:32017125-32017125p.A200V3
chr22:32017847-32017847p.T82A2
chr22:32016634-32016634p.R270W2
chr22:32017023-32017023p.S234Y2
chr22:32021760-32021760p.R14R2
chr22:32017705-32017705p.R129H2
chr22:32016555-32016555p.R296H1
chr22:32017126-32017126p.A200S1

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample22 81 1 1   11  110 6
# mutation22 61 1 1   11  19 6
nonsynonymous SNV1  41   1   1   15 4
synonymous SNV12 2  1      1   4 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])

Top
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
chr22:32015676p.F350F3
chr22:32017125p.A200V3
chr22:32016599p.F356L1
chr22:32017778p.R188H1
chr22:32015655p.S183L1
chr22:32016634p.E339K1
chr22:32017780p.P141P1
chr22:32015660p.R332H1
chr22:32017070p.L139L1
chr22:32017782p.G328G1

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 PISD 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]

Top
Gene Expression for PISD

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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
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

GUCD1,C2orf50,CCDC117,CCDC64,CNTD1,COQ6,CST9,
CYB5R1,FBP1,ITPKA,IVD,KIAA1467,MAPK3,MEAF6,
MLPH,NECAB3,NPTX1,PISD,SLC27A4,SYNGR1,SYTL4
AIFM2,ALDH4A1,BCAP31,BHMT2,NPR3,CES1,CES1P1,
DHDDS,ELMOD3,EPB41L1,FADS3,GCOM1,HSPA12A,ITPK1,
KANK4,LEP,MYO1C,PISD,PYGL,SNN,TNIP1

ASCC2,CHEK2,DRG1,FBXO7,NOL12,PES1,PISD,
PITPNB,RANBP1,RHBDD3,RPS19BP1,SNRPD3,THAP7,THOC5,
TOP3B,TRMT2A,TRMU,UBE2L3,UFD1L,UQCR10,YDJC
AFMID,BNIP1,C12orf66,COA1,TRMT13,CPSF4,CTNNBIP1,
HSCB,KCTD6,GPALPP1,ICE2,NSUN4,NUPL2,PCID2,
PDCD2,PISD,PRMT6,RPAIN,TBP,TMEM218,ZNF273
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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for PISD
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00144phosphatidylserine decarboxylaseapproved; nutraceuticalPhosphatidylserine


Top
Cross referenced IDs for PISD
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas