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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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TissGeneSummary

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TissGeneExp

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TissGene-miRNA

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TissGeneMut: TissGeneSNV, TissGeneCNV, and TissGeneFusions

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TissGeneNet

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TissGeneProg

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TissGeneClin: TissGeneDrug and TissGeneDisease

TissGeneSummary for SCP2
check button Gene summary
Basic gene informationGene symbolSCP2
Gene namesterol carrier protein 2
SynonymsNLTP|NSL-TP|SCP-2|SCP-CHI|SCP-X|SCPX
CytomapUCSC genome browser: 1p32
Type of geneprotein-coding
RefGenesNM_001007098.2,
NM_001007099.2,NM_001007100.2,NM_001007250.2,NM_001193599.1,
NM_001193600.1,NM_001193617.1,NM_002979.4,
Descriptionnon-specific lipid-transfer proteinpropanoyl-CoA C-acyltransferasesterol carrier protein X
Modification date20141207
dbXrefs MIM : 184755
HGNC : HGNC
Ensembl : ENSG00000116171
HPRD : 01700
Vega : OTTHUMG00000008936
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SCP2
BioGPS: 6342
PathwayNCI Pathway Interaction Database: SCP2
KEGG: SCP2
REACTOME: SCP2
Pathway Commons: SCP2
ContextiHOP: SCP2
ligand binding site mutation search in PubMed: SCP2
UCL Cancer Institute: SCP2
Assigned class in TissGDB*C
Included tissue-specific gene expression resourcesTiGER,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)BladderBone marrowLiver
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)BLCALAMLLIHC
Reference showing the relevant tissue of SCP2
Description by TissGene annotationsFused withOncogene
* 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.

check button Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO termPubMed ID
GO:0006694steroid biosynthetic process1703300
GO:0006701progesterone biosynthetic process1703300
GO:0015914phospholipid transport12641450
GO:0032385positive regulation of intracellular cholesterol transport15449949
GO:0032959inositol trisphosphate biosynthetic process12641450
GO:0045940positive regulation of steroid metabolic process1703300
GO:0072659protein localization to plasma membrane12641450
GO:1901373lipid hydroperoxide transport15449949
GO:0006694steroid biosynthetic process1703300
GO:0006701progesterone biosynthetic process1703300
GO:0015914phospholipid transport12641450
GO:0032385positive regulation of intracellular cholesterol transport15449949
GO:0032959inositol trisphosphate biosynthetic process12641450
GO:0045940positive regulation of steroid metabolic process1703300
GO:0072659protein localization to plasma membrane12641450
GO:1901373lipid hydroperoxide transport15449949


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TissGeneExp for SCP2

check button 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 exp


check button 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 isoform exp


check button 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.
normal gene exp


check button 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)
DEG exp

- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05)
Cancer typeMean(exp) in tumorMean(exp) in matched normalLog2FCP-val.FDR
LIHC2.8738334944.272015494-1.3981827.13E-121.18E-10


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TissGene-miRNA for SCP2

check button 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 typemiRNA idmiRNA accessionP-val.Coeff.# samples


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TissGeneMut for SCP2
TissGeneSNV for SCP2

check button 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.
SNV lollipop
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check button 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)
SNV distribution

- nsSNVs sorted by frequency.
AAchangeCancer type# samples
p.E258*UCEC3
p.A387SLUAD1
p.E312KUCEC1
p.G246DPAAD1
p.A104TLGG1
p.E258ASTAD1
p.Q51HCESC1
p.H78YKIRP1
p.P346SSKCM1
p.I108THNSC1
p.R286*LUSC1
p.D306NUCEC1
p.R136KLUAD1
p.P264SSKCM1
p.M280ILUAD1
p.G334*UCEC1
p.M280IESCA1
p.A237VHNSC1
p.Y174CLUAD1
p.S190ICOAD1
p.A532TSKCM1
p.C225WLIHC1
p.P183SSKCM1
p.E449KBLCA1
p.S352LSKCM1
p.G527DPRAD1
p.E30DUCEC1
p.A75VUCEC1
p.E172KSKCM1
p.M529IPCPG1
p.H189NUCEC1
p.G127RSKCM1
p.A95TSKCM1
p.D262YUCEC1
p.V301ISTAD1
p.E253KSKCM1
p.P346LSKCM1
p.T509ASTAD1
p.M529KKIRC1
p.L444PSTAD1
p.L46RBLCA1
p.R105GUCS1
p.P265LSKCM1
p.I76VSKCM1
p.E231XCOAD1
p.G165DPAAD1
p.K353NCHOL1
p.H54YKIRP1
p.G46RSKCM1
p.F518LESCA1
p.S502*SKCM1
p.Q73HBLCA1
p.A359TPRAD1


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TissGeneCNV for SCP2

check button 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)
CNV


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TissGeneFusions for SCP2

check button Fusion genes including TissGene
(ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01)
DatabaseSrcCancer typeSampleFusion geneORF5'-gene BP3'-gene BP
Chimerdb3.0ChiTaRsNAAI082430SCP2-PJA2chr1:53517282chr5:108714077
Chimerdb3.0FusionScanESCATCGA-LN-A49L-01ARRAS2-SCP2Out-of-Framechr11:14303147chr1:53458929
Chimerdb3.0FusionScanESCATCGA-IG-A3I8-01ARRAS2-SCP2Out-of-Framechr11:14303147chr1:53458929
Chimerdb3.0FusionScanESCATCGA-LN-A8I0-01ARRAS2-SCP2Out-of-Framechr11:14303147chr1:53458929
Chimerdb3.0FusionScanESCATCGA-JY-A6FB-01ARRAS2-SCP2Out-of-Framechr11:14303147chr1:53458929
Chimerdb3.0FusionScanESCATCGA-LN-A4A9-01ARRAS2-SCP2Out-of-Framechr11:14303147chr1:53458929
Chimerdb3.0FusionScanESCATCGA-IG-A3I8-11ARRAS2-SCP2Out-of-Framechr11:14303147chr1:53458929
Chimerdb3.0FusionScanESCATCGA-JY-A6FA-01ARRAS2-SCP2Out-of-Framechr11:14303147chr1:53458929
TCGAfusionPortalPRADABRCATCGA-E2-A1IH-01ASCP2-ECHDC2In-frameChr1:53393137Chr1:53364896
TCGAfusionPortalPRADALUADTCGA-NJ-A4YF-01ACPT2-SCP2In-frameChr1:53676991Chr1:53420412


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TissGeneNet for SCP2

check button 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)
BRCA (tumor)BRCA (normal)
SCP2, ELAVL1, CACNA1A, CAV1, EPB41, PHYH, TYSND1, PITPNA, ACOX1, ACAA2, EHHADH (tumor)SCP2, ELAVL1, CACNA1A, CAV1, EPB41, PHYH, TYSND1, PITPNA, ACOX1, ACAA2, EHHADH (normal)
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COAD (tumor)COAD (normal)
SCP2, ELAVL1, CACNA1A, CAV1, EPB41, PHYH, TYSND1, PITPNA, ACOX1, ACAA2, EHHADH (tumor)SCP2, ELAVL1, CACNA1A, CAV1, EPB41, PHYH, TYSND1, PITPNA, ACOX1, ACAA2, EHHADH (normal)
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HNSC (tumor)HNSC (normal)
SCP2, ELAVL1, CACNA1A, CAV1, EPB41, PHYH, TYSND1, PITPNA, ACOX1, ACAA2, EHHADH (tumor)SCP2, ELAVL1, CACNA1A, CAV1, EPB41, PHYH, TYSND1, PITPNA, ACOX1, ACAA2, EHHADH (normal)
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KICH (tumor)KICH (normal)
SCP2, ELAVL1, CACNA1A, CAV1, EPB41, PHYH, TYSND1, PITPNA, ACOX1, ACAA2, EHHADH (tumor)SCP2, ELAVL1, CACNA1A, CAV1, EPB41, PHYH, TYSND1, PITPNA, ACOX1, ACAA2, EHHADH (normal)
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KIRC (tumor)KIRC (normal)
SCP2, ELAVL1, CACNA1A, CAV1, EPB41, PHYH, TYSND1, PITPNA, ACOX1, ACAA2, EHHADH (tumor)SCP2, ELAVL1, CACNA1A, CAV1, EPB41, PHYH, TYSND1, PITPNA, ACOX1, ACAA2, EHHADH (normal)
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KIRP (tumor)KIRP (normal)
SCP2, ELAVL1, CACNA1A, CAV1, EPB41, PHYH, TYSND1, PITPNA, ACOX1, ACAA2, EHHADH (tumor)SCP2, ELAVL1, CACNA1A, CAV1, EPB41, PHYH, TYSND1, PITPNA, ACOX1, ACAA2, EHHADH (normal)
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LIHC (tumor)LIHC (normal)
SCP2, ELAVL1, CACNA1A, CAV1, EPB41, PHYH, TYSND1, PITPNA, ACOX1, ACAA2, EHHADH (tumor)SCP2, ELAVL1, CACNA1A, CAV1, EPB41, PHYH, TYSND1, PITPNA, ACOX1, ACAA2, EHHADH (normal)
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LUAD (tumor)LUAD (normal)
SCP2, ELAVL1, CACNA1A, CAV1, EPB41, PHYH, TYSND1, PITPNA, ACOX1, ACAA2, EHHADH (tumor)SCP2, ELAVL1, CACNA1A, CAV1, EPB41, PHYH, TYSND1, PITPNA, ACOX1, ACAA2, EHHADH (normal)
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LUSC (tumor)LUSC (normal)
SCP2, ELAVL1, CACNA1A, CAV1, EPB41, PHYH, TYSND1, PITPNA, ACOX1, ACAA2, EHHADH (tumor)SCP2, ELAVL1, CACNA1A, CAV1, EPB41, PHYH, TYSND1, PITPNA, ACOX1, ACAA2, EHHADH (normal)
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PRAD (tumor)PRAD (normal)
SCP2, ELAVL1, CACNA1A, CAV1, EPB41, PHYH, TYSND1, PITPNA, ACOX1, ACAA2, EHHADH (tumor)SCP2, ELAVL1, CACNA1A, CAV1, EPB41, PHYH, TYSND1, PITPNA, ACOX1, ACAA2, EHHADH (normal)
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STAD (tumor)STAD (normal)
SCP2, ELAVL1, CACNA1A, CAV1, EPB41, PHYH, TYSND1, PITPNA, ACOX1, ACAA2, EHHADH (tumor)SCP2, ELAVL1, CACNA1A, CAV1, EPB41, PHYH, TYSND1, PITPNA, ACOX1, ACAA2, EHHADH (normal)
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THCA (tumor)THCA (normal)
SCP2, ELAVL1, CACNA1A, CAV1, EPB41, PHYH, TYSND1, PITPNA, ACOX1, ACAA2, EHHADH (tumor)SCP2, ELAVL1, CACNA1A, CAV1, EPB41, PHYH, TYSND1, PITPNA, ACOX1, ACAA2, EHHADH (normal)
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TissGeneProg for SCP2

check button 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.
survival 1

check button 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.
survival 2

check button 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.
survival 3

check button 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.
survival 4

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TissGeneClin for SCP2
TissGeneDrug for SCP2

check button Drug information targeting TissGene
(DrugBank Version 5.0.6, 2017-04-01)
DrugBank IDDrug nameDrug activityDrug typeDrug status


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TissGeneDisease for SCP2

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0023903Liver neoplasms2BeFree
umls:C0856727Cholesterol gallstones2BeFree
umls:C2239176Liver carcinoma2BeFree
umls:C0002395Alzheimer's Disease1BeFree
umls:C0004352Autistic Disorder1GAD
umls:C0011853Diabetes Mellitus, Experimental1RGD
umls:C0013421Dystonia1BeFree,CTD_human
umls:C0027404Narcolepsy1GAD
umls:C0152025Polyneuropathy1CTD_human
umls:C0206686Adrenocortical carcinoma1BeFree
umls:C0235025Peripheral motor neuropathy1BeFree
umls:C0270612Leukoencephalopathies1CTD_human
umls:C0393593Dystonia Disorders1BeFree
umls:C1859133RHIZOMELIC CHONDRODYSPLASIA PUNCTATA, TYPE 11BeFree
umls:C2745900Promyelocytic leukemia1BeFree
umls:C3150990LEUKOENCEPHALOPATHY WITH DYSTONIA AND MOTOR NEUROPATHY0CLINVAR,CTD_human,ORPHANET