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 PITPNB
Basic gene info.Gene symbolPITPNB
Gene namephosphatidylinositol transfer protein, beta
SynonymsPI-TP-beta|PtdInsTP|VIB1B
CytomapUCSC genome browser: 22q12.1
Genomic locationchr22 :28247656-28315255
Type of geneprotein-coding
RefGenesNM_001284277.1,
NM_001284278.1,NM_012399.4,
Ensembl idENSG00000180957
DescriptionPtdIns transfer protein betaphosphatidylinositol transfer protein beta isoformphosphotidylinositol transfer protein, beta
Modification date20141207
dbXrefs MIM : 606876
HGNC : HGNC
Ensembl : ENSG00000180957
HPRD : 06044
Vega : OTTHUMG00000150976
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PITPNB
BioGPS: 23760
Gene Expression Atlas: ENSG00000180957
The Human Protein Atlas: ENSG00000180957
PathwayNCI Pathway Interaction Database: PITPNB
KEGG: PITPNB
REACTOME: PITPNB
ConsensusPathDB
Pathway Commons: PITPNB
MetabolismMetaCyc: PITPNB
HUMANCyc: PITPNB
RegulationEnsembl's Regulation: ENSG00000180957
miRBase: chr22 :28,247,656-28,315,255
TargetScan: NM_001284277
cisRED: ENSG00000180957
ContextiHOP: PITPNB
cancer metabolism search in PubMed: PITPNB
UCL Cancer Institute: PITPNB
Assigned class in ccmGDBC

Top
Phenotypic Information for PITPNB(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PITPNB
Familial Cancer Database: PITPNB
* 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_PHOSPHOLIPID_METABOLISM
REACTOME_PI_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

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

Mutations for PITPNB
* 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
* 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryPITPNBchr222831423228314252TTC28-AS1chr222833720628337226
pancreasPITPNBchr222828380928283829EWSR1chr222968732829687348
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 PITPNB related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF741687VPS13D1015611247675412516087PITPNB144215222825443128254502
DB095411PITPNB1253222830695228315235CCDC117252554222917693429179571
AI863682PITPNB1241222827503328275273ARHGEF182353871975129367513088
BF916396PITPNB1166222824799728248162ARHGDIB162247121509537115095456
BQ314453DFNB311051369117181109117181140PITPNB131274222825630228256444

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 2 2      
GAIN (# sample)        1        
LOSS (# sample)      1 1 2      
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=3

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=16)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr22:28269793-28269793p.A156D2
chr22:28306975-28306975p.T58T2
chr22:28307060-28307060p.S30N2
chr22:28256204-28256204p.C187F1
chr22:28292602-28292602p.K104Q1
chr22:28310333-28310333p.R8H1
chr22:28256213-28256213p.S184N1
chr22:28292612-28292612p.N100N1
chr22:28315170-28315170p.I4F1
chr22:28269752-28269752p.R170G1

Top
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
# sample 1 81 1 1  21   32 3
# mutation 1 71 1 1  21   32 3
nonsynonymous SNV   31 1 1   1   32 3
synonymous SNV 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
chr22:28306975p.T58T,PITPNB2
chr22:28290544p.E112K,PITPNB1
chr22:28292561p.I111I,PITPNB1
chr22:28306976p.K104Q,PITPNB1
chr22:28292563p.T99T,PITPNB1
chr22:28307087p.P77P,PITPNB1
chr22:28292578p.R73S,PITPNB1
chr22:28310311p.V68L,PITPNB1
chr22:28292579p.T239T,PITPNB1
chr22:28310333p.H63Y,PITPNB1

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 PITPNB 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 PITPNB

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

ADSL,CDC45,CHEK2,DRG1,EIF4ENIF1,FBXO7,HIRA,
JOSD1,LIMK2,MAPK1,NF2,NUP50,PHF5A,PITPNB,
RANBP1,MIEF1,SRRD,THOC5,TUG1,XRCC6,YWHAH
ABCE1,ACTR3,MCMBP,CTSO,CTTNBP2NL,ERI1,GNAI3,
GOLPH3,HIAT1,HIATL1,MAK16,NRAS,NUDCD1,NUS1,
PITPNB,RAB11A,SSR1,TM9SF3,UBLCP1,UFM1,YES1

BCL2L13,CCDC117,CHEK2,DRG1,EIF4ENIF1,FBXO7,HIRA,
HMGXB4,MAPK1,PES1,PISD,PITPNB,RANBP1,SNAP29,
SNRPD3,SRRD,TFIP11,THOC5,UBE2L3,UFD1L,YWHAH
C1orf216,CALU,CLIP4,COPZ2,DENND5A,FGF2,KLHL5,
MAP9,PITPNB,PLS3,QKI,RAB23,IFT22,RASSF8,
RBMS1,RDX,RHOQ,SAE1,SPG20,STX2,ZEB1
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 PITPNB


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