Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 PATL1
Basic gene info.Gene symbolPATL1
Gene nameprotein associated with topoisomerase II homolog 1 (yeast)
SynonymsPat1b|hPat1b
CytomapUCSC genome browser: 11q12.1
Genomic locationchr11 :59404191-59436511
Type of geneprotein-coding
RefGenesNM_152716.2,
Ensembl idENSG00000166889
DescriptionPAT1-like protein 1protein PAT1 homolog 1protein PAT1 homolog b
Modification date20141207
dbXrefs MIM : 614660
HGNC : HGNC
Ensembl : ENSG00000166889
HPRD : 08214
Vega : OTTHUMG00000167423
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PATL1
BioGPS: 219988
Gene Expression Atlas: ENSG00000166889
The Human Protein Atlas: ENSG00000166889
PathwayNCI Pathway Interaction Database: PATL1
KEGG: PATL1
REACTOME: PATL1
ConsensusPathDB
Pathway Commons: PATL1
MetabolismMetaCyc: PATL1
HUMANCyc: PATL1
RegulationEnsembl's Regulation: ENSG00000166889
miRBase: chr11 :59,404,191-59,436,511
TargetScan: NM_152716
cisRED: ENSG00000166889
ContextiHOP: PATL1
cancer metabolism search in PubMed: PATL1
UCL Cancer Institute: PATL1
Assigned class in ccmGDBC

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Phenotypic Information for PATL1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PATL1
Familial Cancer Database: PATL1
* 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_MRNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PATL1
MedGen: PATL1 (Human Medical Genetics with Condition)
ClinVar: PATL1
PhenotypeMGI: PATL1 (International Mouse Phenotyping Consortium)
PhenomicDB: PATL1

Mutations for PATL1
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PATL1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF911667TRIM1412019100848160100848360PATL1192350115940441059404568
BF911658TRIM1412029100848160100848360PATL1193352115940441059404568

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              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)

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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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=43)
Stat. for Synonymous SNVs
(# total SNVs=9)
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
chr11:59423201-59423201p.R276W2
chr11:59421493-59421493p.R362C2
chr11:59416982-59416982p.I562M2
chr11:59423511-59423511p.S244F2
chr11:59423089-59423089p.P313Q2
chr11:59425199-59425199p.?2
chr11:59418265-59418265p.R516*1
chr11:59425037-59425037p.P196H1
chr11:59406615-59406615p.L733M1
chr11:59420456-59420456p.G386E1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample11 3  2    331  11617
# mutation11 3  2    431  117112
nonsynonymous SNV 1 3  2    21   82111
synonymous SNV1          221  35 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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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
chr11:59416982p.I562M2
chr11:59423511p.S244F2
chr11:59420467p.D567V1
chr11:59415331p.G386E1
chr11:59425039p.R171Q1
chr11:59420024p.Y566Y1
chr11:59420470p.R385K1
chr11:59415336p.P162S1
chr11:59425053p.A382A1
chr11:59420040p.L78V1

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 PATL1 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 PATL1

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

ASPM,BUB1,CENPI,CKAP2L,DBF4,GMPS,INCENP,
KIF18A,MSH2,NCAPG2,NUP205,PATL1,POLQ,R3HDM1,
SGOL1,SGOL2,STIL,TTK,XPO1,XRCC2,ZFP91
APPL1,ARIH1,CUL3,DYRK1A,FASTKD2,IBTK,MED14,
NEDD1,OTUD4,PATL1,PCM1,RBL1,REV1,RINT1,
SACS,SOS2,TNKS2,TPP2,UBE3A,USP15,ZRANB1

CDCA5,CHEK1,CKAP2L,CKAP5,CPSF7,E2F8,FAM111B,
FBXO45,HELLS,HNRNPR,INCENP,KIF15,MKI67,MSH2,
NCAPD3,NUP98,OSBP,PATL1,SSRP1,STIL,STX3
ABHD2,ADAR,AP1G1,AP3B1,AP3D1,BAZ1A,BIRC6,
CHD1,CLTC,CSNK1G1,DLG3,GTPBP1,NCOR1,PATL1,
RCOR1,RNF213,SAP130,SEC24C,TOP1,TOP1P1,UBR2
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 PATL1


There's no related Drug.
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Cross referenced IDs for PATL1
* 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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