TissGeneSummary for PSD2 |
Gene summary |
Basic gene information | Gene symbol | PSD2 |
Gene name | pleckstrin and Sec7 domain containing 2 | |
Synonyms | EFA6C | |
Cytomap | UCSC genome browser: 5q31.2 | |
Type of gene | protein-coding | |
RefGenes | NM_032289.2, | |
Description | 6330404E20RikPH and SEC7 domain-containing protein 2pleckstrin homology and SEC7 domain-containing protein 2 | |
Modification date | 20141207 | |
dbXrefs | HGNC : HGNC | |
Ensembl : ENSG00000146005 | ||
HPRD : 15190 | ||
Vega : OTTHUMG00000129240 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PSD2 | |
BioGPS: 84249 | ||
Pathway | NCI Pathway Interaction Database: PSD2 | |
KEGG: PSD2 | ||
REACTOME: PSD2 | ||
Pathway Commons: PSD2 | ||
Context | iHOP: PSD2 | |
ligand binding site mutation search in PubMed: PSD2 | ||
UCL Cancer Institute: PSD2 | ||
Assigned class in TissGDB* | C | |
Included tissue-specific gene expression resources | HPA,TiGER | |
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx) | Brain | |
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | GBM,LGG | |
Reference showing the relevant tissue of PSD2 | ||
Description by TissGene annotations | Have significant anti-correlated miRNA TissgsKTS CNV lost TissGeneKTS |
* Class A consists of genes with literature evidence and is part of the cTissGenes. Class B consists of only cTissGenes without additional evidence. The remaining genes belong to Class C. |
Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
GO ID | GO term | PubMed ID |
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TissGeneExp for PSD2 |
Gene expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) |
Gene isoform expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA pan-cancer tcga_rsem_isoform_tpm, version 2016-09-01) |
Gene expressions across normal tissues of GTEx data (GTEx GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct) - Here, we shows the matched tissue types only among our 28 cancer types. |
Different expressions across 14 cancer types with more than 10 samples between matched tumors and normals (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) |
- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05) |
Cancer type | Mean(exp) in tumor | Mean(exp) in matched normal | Log2FC | P-val. | FDR |
PRAD | -1.846822989 | -0.831690297 | -1.015132692 | 4.83E-10 | 8.52E-09 |
KIRC | -0.363510276 | -2.081982498 | 1.718472222 | 1.75E-13 | 7.94E-13 |
BRCA | -1.380074676 | 0.829954271 | -2.210028947 | 6.65E-23 | 5.83E-22 |
THCA | -0.407671881 | -1.901661712 | 1.493989831 | 3.38E-10 | 2.09E-09 |
HNSC | -2.59187129 | -1.491996871 | -1.099874419 | 0.000602 | 0.002184677 |
KICH | -0.51852822 | -1.87807622 | 1.359548 | 0.00067 | 0.001493104 |
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TissGene-miRNA for PSD2 |
Significantly anti-correlated miRNAs of TissGene across 28 cancer types (Gene-miRNA relations from TargetScanHuman Relsease 7.1, Conserved_Site_Context_Scores.txt.zip, 06.01.2016) (TCGA IlluminaHiSeq_miRNASeq, log2(RPM+1) data, version 2016-11-21) (TCGA IlluminaHiSeq_RNASeqV2, log2(normalized_count+1) data, version 2016-08-16) (Spearman’s Rank Correlation (p-value<0.05 and coefficient<-0.25)) |
Cancer type | miRNA id | miRNA accession | P-val. | Coeff. | # samples |
ACC | hsa-miR-410-3p | MIMAT0002171 | 0.021 | -0.26 | 78 |
ACC | hsa-miR-410-3p | MIMAT0002171 | 0.021 | -0.26 | 78 |
UVM | hsa-miR-199b-3p | MIMAT0004563 | 0.006 | -0.31 | 80 |
UVM | hsa-miR-199a-3p | MIMAT0000232 | 0.006 | -0.31 | 80 |
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TissGeneMut for PSD2 |
TissGeneSNV for PSD2 |
nsSNV counts per each loci. Different colors of circles represent different cancer types. Circle size denotes number of samples. (TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25) * Click on the image to enlarge it in a new window. |
Somatic nucleotide variants of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of mutated samples) The numbers in parentheses are numbers of samples with mutation (nsSNVs). (TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25) |
- nsSNVs sorted by frequency. |
AAchange | Cancer type | # samples |
p.S402L | UCEC | 2 |
p.E130X | ESCA | 1 |
p.E349V | SARC | 1 |
p.R728W | STAD | 1 |
p.R230H | UCEC | 1 |
p.L303V | BLCA | 1 |
p.R50Q | SKCM | 1 |
p.Q669H | ESCA | 1 |
p.P302L | HNSC | 1 |
p.Q154X | READ | 1 |
p.S292L | STAD | 1 |
p.G207E | SKCM | 1 |
p.Y558C | LUSC | 1 |
p.P373Q | LUAD | 1 |
p.S8P | PRAD | 1 |
p.D765N | SKCM | 1 |
p.E293D | LGG | 1 |
p.A139T | STAD | 1 |
p.S565L | READ | 1 |
p.P179S | LUAD | 1 |
p.A211E | HNSC | 1 |
p.R329C | STAD | 1 |
p.E611K | SKCM | 1 |
p.R18C | LIHC | 1 |
p.E130K | SKCM | 1 |
p.E95K | SKCM | 1 |
p.S8P | STAD | 1 |
p.V133L | COAD | 1 |
p.F68L | HNSC | 1 |
p.K62N | STAD | 1 |
p.A105V | COAD | 1 |
p.L714I | SARC | 1 |
p.R224H | BLCA | 1 |
p.D355N | BLCA | 1 |
p.F205I | LIHC | 1 |
p.F542L | LUSC | 1 |
p.R230C | LUAD | 1 |
p.H315Y | CESC | 1 |
p.R134W | STAD | 1 |
p.R134W | ESCA | 1 |
p.K541N | UCEC | 1 |
p.D159Y | LUAD | 1 |
p.P64S | SKCM | 1 |
p.R390L | MESO | 1 |
p.D599N | STAD | 1 |
p.R316W | SKCM | 1 |
p.R574C | BLCA | 1 |
p.S292* | UCEC | 1 |
p.R644W | SKCM | 1 |
p.L714I | UCS | 1 |
p.E465D | COAD | 1 |
p.H315D | BLCA | 1 |
p.Q656K | LUAD | 1 |
p.R334W | UCEC | 1 |
p.G294E | SKCM | 1 |
p.P20L | SARC | 1 |
p.S165N | SKCM | 1 |
p.A672S | LUAD | 1 |
p.R494* | LGG | 1 |
p.R224C | LUSC | 1 |
p.P533T | PRAD | 1 |
p.R134Q | SKCM | 1 |
p.E142D | UCEC | 1 |
p.G47E | SKCM | 1 |
p.P182L | KIRC | 1 |
p.P397H | COAD | 1 |
p.T549I | SKCM | 1 |
p.R50Q | LGG | 1 |
p.E130* | ESCA | 1 |
p.A82V | SKCM | 1 |
p.F502S | LIHC | 1 |
p.D171N | SKCM | 1 |
p.G486W | KIRP | 1 |
p.R494Q | STAD | 1 |
p.A731V | THYM | 1 |
p.R187Q | COAD | 1 |
p.K596N | LUAD | 1 |
p.E341K | SKCM | 1 |
p.V518I | UCEC | 1 |
p.R695Q | STAD | 1 |
p.R644W | LIHC | 1 |
p.G84W | LUSC | 1 |
p.P645H | LUAD | 1 |
p.R187W | THYM | 1 |
p.R531K | SKCM | 1 |
p.S357L | STAD | 1 |
p.R320L | LUAD | 1 |
p.T418M | READ | 1 |
p.G548E | SKCM | 1 |
p.C307F | COAD | 1 |
p.A94V | LIHC | 1 |
p.E91K | SKCM | 1 |
p.G254S | SKCM | 1 |
p.P116T | LIHC | 1 |
p.D168E | SKCM | 1 |
p.D267A | PRAD | 1 |
p.I459M | BLCA | 1 |
p.R534S | COAD | 1 |
p.D86Y | STAD | 1 |
p.R320H | UCEC | 1 |
p.E657D | READ | 1 |
p.D355N | UCEC | 1 |
p.E177* | LIHC | 1 |
p.T493M | LUSC | 1 |
p.K530R | OV | 1 |
p.D132N | BLCA | 1 |
p.L503P | LUAD | 1 |
p.E177X | LIHC | 1 |
p.R189H | STAD | 1 |
p.S458F | UCEC | 1 |
p.R661Q | LIHC | 1 |
p.A544T | UCEC | 1 |
p.V682I | SKCM | 1 |
p.R383Q | BRCA | 1 |
p.K610N | THYM | 1 |
p.R329L | BLCA | 1 |
p.A204V | LUAD | 1 |
p.R316W | BLCA | 1 |
p.D599N | BLCA | 1 |
p.G163R | BRCA | 1 |
p.Q554H | COAD | 1 |
p.G444D | LIHC | 1 |
p.R537H | SARC | 1 |
p.S113N | SKCM | 1 |
p.G127C | THYM | 1 |
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TissGeneCNV for PSD2 |
Copy number variations of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of CNV samples) (TCGA Gistic2_CopyNumber_Gistic2_all_data_by_genes, Gistic2 copy number data, version 2016-08-16) |
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TissGeneFusions for PSD2 |
Fusion genes including TissGene (ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01) |
Database | Src | Cancer type | Sample | Fusion gene | ORF | 5'-gene BP | 3'-gene BP |
TCGAfusionPortal | PRADA | BRCA | TCGA-BH-A0B3-01A | NCOA1-PSD2 | 5UTR-CDS | Chr2:24787299 | Chr5:139201478 |
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TissGeneNet for PSD2 |
Co-expressed gene networks based on protein-protein interaction data (CePIN) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (PINA2 ppi data) |
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TissGeneProg for PSD2 |
Kaplan-Meier plots with logrank tests of overall survival (OS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image to enlarge it in a new window. |
Kaplan-Meier plots with logrank test of relapse free survival (RFS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
Forest plot of Cox proportional hazard ratio (HR) and 95% CI of overall survival (OS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
Forest plot of Cox proportional hazard ratio (HR) and 95% CI of relapse free survival (RFS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
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TissGeneClin for PSD2 |
TissGeneDrug for PSD2 |
Drug information targeting TissGene (DrugBank Version 5.0.6, 2017-04-01) |
DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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TissGeneDisease for PSD2 |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C0032927 | Precancerous Conditions | 1 | CTD_human |