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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 LECT2
check button Gene summary
Basic gene informationGene symbolLECT2
Gene nameleukocyte cell-derived chemotaxin 2
Synonymschm-II|chm2
CytomapUCSC genome browser: 5q31.1
Type of geneprotein-coding
RefGenesNM_002302.2,
Descriptionchondromodulin-IIleukocyte cell-derived chemotaxin-2
Modification date20141207
dbXrefs MIM : 602882
HGNC : HGNC
Ensembl : ENSG00000145826
HPRD : 04196
Vega : OTTHUMG00000129146
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LECT2
BioGPS: 3950
PathwayNCI Pathway Interaction Database: LECT2
KEGG: LECT2
REACTOME: LECT2
Pathway Commons: LECT2
ContextiHOP: LECT2
ligand binding site mutation search in PubMed: LECT2
UCL Cancer Institute: LECT2
Assigned class in TissGDB*A
Included tissue-specific gene expression resourcesHPA,TiGER,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)Liver
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)LIHC
Reference showing the relevant tissue of LECT2Functional diets modulate the acute phase protein response in Oncorhynchus mykiss subjected to chronic stress and challenged with Vibrio anguillarum. Castro-Osses D, Carrera-Naipil C, Gallardo-Escárate C, Gonçalves AT. Fish Shellfish Immunol. 2017 Jul;66:62-70. doi: 10.1016/j.fsi.2017.05.001. Epub 2017 May 2. (pmid:28476670)
go to article
Description by TissGene annotationsTissgsKTS
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.

check button Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO termPubMed ID


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TissGeneExp for LECT2

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
LIHC7.63850647110.72074047-3.0822343.53E-072.14E-06


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TissGene-miRNA for LECT2

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 LECT2
TissGeneSNV for LECT2

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.P113HUCEC2
p.A68PBLCA1
p.G19VLUAD1
p.Q82*SKCM1
p.G112DSKCM1
p.R92*SKCM1
p.K109NBLCA1
p.K115ESKCM1
p.P69LSKCM1
p.C25YHNSC1
p.C25YLUAD1
p.E32DBLCA1
p.T15ILUAD1
p.I58SUCEC1
p.Q82XSKCM1
p.I13FUCEC1
p.G76ROV1
p.Y104CKICH1
p.G27VCOAD1
p.E78DUCEC1
p.Y110NLUAD1
p.Y44FSKCM1
p.S3CBLCA1
p.F98YSKCM1
p.K115TUCEC1
p.E140KBLCA1
p.K84NHNSC1
p.E32KTHYM1
p.P125HLUAD1
p.Q74PUCEC1
p.R92XSKCM1


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TissGeneCNV for LECT2

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 LECT2

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


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TissGeneNet for LECT2

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)
LECT2, HDAC1 (tumor)LECT2, HDAC1 (normal)
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COAD (tumor)COAD (normal)
LECT2, HDAC1 (tumor)LECT2, HDAC1 (normal)
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HNSC (tumor)HNSC (normal)
LECT2, HDAC1 (tumor)LECT2, HDAC1 (normal)
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KICH (tumor)KICH (normal)
LECT2, HDAC1 (tumor)LECT2, HDAC1 (normal)
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KIRC (tumor)KIRC (normal)
LECT2, HDAC1 (tumor)LECT2, HDAC1 (normal)
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KIRP (tumor)KIRP (normal)
LECT2, HDAC1 (tumor)LECT2, HDAC1 (normal)
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LIHC (tumor)LIHC (normal)
LECT2, HDAC1 (tumor)LECT2, HDAC1 (normal)
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LUAD (tumor)LUAD (normal)
LECT2, HDAC1 (tumor)LECT2, HDAC1 (normal)
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LUSC (tumor)LUSC (normal)
LECT2, HDAC1 (tumor)LECT2, HDAC1 (normal)
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PRAD (tumor)PRAD (normal)
LECT2, HDAC1 (tumor)LECT2, HDAC1 (normal)
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STAD (tumor)STAD (normal)
LECT2, HDAC1 (tumor)LECT2, HDAC1 (normal)
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THCA (tumor)THCA (normal)
LECT2, HDAC1 (tumor)LECT2, HDAC1 (normal)
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TissGeneProg for LECT2

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 LECT2
TissGeneDrug for LECT2

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 LECT2

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C2239176Liver carcinoma3BeFree
umls:C0028754Obesity2BeFree
umls:C0002726Amyloidosis1BeFree
umls:C0003873Rheumatoid Arthritis1BeFree
umls:C0015695Fatty Liver1BeFree
umls:C0020459Hyperinsulinism1BeFree
umls:C0023290Leishmaniasis, Visceral1BeFree
umls:C0023903Liver neoplasms1BeFree
umls:C0085605Liver Failure1LHGDN
umls:C0206624Hepatoblastoma1BeFree
umls:C0268382Amyloid nephropathy1BeFree
umls:C0341439Chronic liver disease1BeFree
umls:C0400966Non-alcoholic Fatty Liver Disease1BeFree
umls:C0403447Chronic Kidney Insufficiency1BeFree
umls:C0746556metabolic disturbance1BeFree
umls:C1512409Hepatocarcinogenesis1BeFree
umls:C1561643Chronic Kidney Diseases1BeFree
umls:C1709246Non-Neoplastic Disorder1BeFree
umls:C2711227Steatohepatitis1BeFree