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 STK11
Basic gene info.Gene symbolSTK11
Gene nameserine/threonine kinase 11
SynonymsLKB1|PJS|hLKB1
CytomapUCSC genome browser: 19p13.3
Genomic locationchr19 :1205797-1228434
Type of geneprotein-coding
RefGenesNM_000455.4,
Ensembl idENSG00000118046
Descriptionliver kinase B1polarization-related protein LKB1renal carcinoma antigen NY-REN-19serine/threonine-protein kinase 11serine/threonine-protein kinase LKB1serine/threonine-protein kinase STK11
Modification date20141222
dbXrefs MIM : 602216
HGNC : HGNC
Ensembl : ENSG00000118046
HPRD : 03740
ProteinUniProt: Q15831
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_STK11
BioGPS: 6794
Gene Expression Atlas: ENSG00000118046
The Human Protein Atlas: ENSG00000118046
PathwayNCI Pathway Interaction Database: STK11
KEGG: STK11
REACTOME: STK11
ConsensusPathDB
Pathway Commons: STK11
MetabolismMetaCyc: STK11
HUMANCyc: STK11
RegulationEnsembl's Regulation: ENSG00000118046
miRBase: chr19 :1,205,797-1,228,434
TargetScan: NM_000455
cisRED: ENSG00000118046
ContextiHOP: STK11
cancer metabolism search in PubMed: STK11
UCL Cancer Institute: STK11
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of STK11 in cancer cell metabolism1. Shackelford DB, Abt E, Gerken L, Vasquez DS, Seki A, et al. (2013) LKB1 inactivation dictates therapeutic response of non-small cell lung cancer to the metabolism drug phenformin. Cancer cell 23: 143-158. go to article
2. Liu Y, Marks K, Cowley GS, Carretero J, Liu Q, et al. (2013) Metabolic and functional genomic studies identify deoxythymidylate kinase as a target in LKB1-mutant lung cancer. Cancer discovery 3: 870-879. go to article
3. Dupuy F, Griss T, Blagih J, Bridon G, Avizonis D, et al. (2013) LKB1 is a central regulator of tumor initiation and pro-growth metabolism in ErbB2-mediated breast cancer. Cancer Metab 1: 18. go to article

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Phenotypic Information for STK11(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: STK11
Familial Cancer Database: STK11
* 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 LUAD 6,

Therapeutic Vulnerabilities in Cancer7

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,
6 http://www.sciencedirect.com/science/article/pii/S0092867412010227,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

check002.gifOthers
OMIM 175200; phenotype.
273300; phenotype.
602216; gene.
Orphanet 2869; Peutz-Jeghers syndrome.
DiseaseKEGG Disease: STK11
MedGen: STK11 (Human Medical Genetics with Condition)
ClinVar: STK11
PhenotypeMGI: STK11 (International Mouse Phenotyping Consortium)
PhenomicDB: STK11

Mutations for STK11
* 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
There's no inter-chromosomal structural variation.
- 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
ovarySTK11chr1912134361213456MED16chr19870704870724
ovarySTK11chr1912153661215386STK11chr1912238941223914
ovarySTK11chr1912247611224781SBNO2chr1911385201138540
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 STK11 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI968661RPP14119535830516558305359STK111903121912246181224740
AI365374RPP14119535830516558305359STK111904461912244841224740

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 # sample          1      
GAIN (# sample)                 
LOSS (# sample)          1      
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=35

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=236)
Stat. for Synonymous SNVs
(# total SNVs=32)
Stat. for Deletions
(# total SNVs=60)
Stat. for Insertions
(# total SNVs=15)

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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
chr19:1223125-1223125p.F354L29
chr19:1221319-1221319p.P281L17
chr19:1206913-1226646p.0?16
chr19:1207021-1207021p.Q37*12
chr19:1220487-1220487p.D194Y9
chr19:1220415-1220415p.Q170*8
chr19:1207092-1207092p.Y60Y7
chr19:1221210-1221210p.?6
chr19:1226570-1226570p.R409Q6
chr19:1221211-1221211p.?4

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample  134  1 31 121   32 1
# mutation  137  2 21 131   32 1
nonsynonymous SNV   22  2 11 13    21 1
synonymous SNV  115    1   1   11  
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
chr19:1226570p.R409Q5
chr19:1219403p.Q152R3
chr19:1207078p.G56W2
chr19:1220416p.Y60Y2
chr19:1207092p.Q170R2
chr19:1220429p.H174H2
chr19:1220699p.R86R1
chr19:1207117p.N181Y1
chr19:1219344p.Y272Y1
chr19:1223111p.Y49H1

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 STK11 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 STK11

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.
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check002.gifProtein Expression Plot (RPPA)
*RPPA protein expression data were extracted from TCPA (The Cancer Proteome Atlas). Normalized data based on replicated based normalization (RBN) was used to draw following figures.

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

ADAT3,BTBD2,TPGS1,C19orf25,CACTIN,TMEM259,CSNK1G2,
ABHD17A,HDGFRP2,KLF16,MBD3,MED16,MIER2,NDUFS7,
POLR2E,POLRMT,RNF126,SIRT6,SPPL2B,STK11,WDR18
ABCF3,ACTR1B,ATP5D,RABL6,CTBP1,EVI5L,CPTP,
HSF1,KEAP1,LONP1,MAP2K2,NTMT1,MIB2,MRPL12,
NDUFV1,NOSIP,POLRMT,PTGES2,SIVA1,STK11,TIMM44

ADAT3,CACTIN,TMEM259,CSNK1G2,DOHH,FZR1,HDGFRP2,
CAMSAP3,MAP2K2,NR2F6,POLRMT,RAVER1,REXO1,RNF126,
SAMD1,SF3A2,SPPL2B,STK11,TCF3,XAB2,ZNF414
ADAT3,VPS51___IFT46,CC2D1A,CCDC61,CTU1,F8A1,FUK,
CPTP,LRFN3,MFSD10,C8orf82,MIB2,PGLS,PLA2G6,
POLRMT,SPNS1,STK11,TAF6L,TIGD5,ZNF672,ZNF787
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 STK11
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB Q15831; -.
ChemistryChEMBL CHEMBL5606; -.
ChemistryGuidetoPHARMACOLOGY 2212; -.
Organism-specific databasesPharmGKB PA36198; -.
Organism-specific databasesCTD 6794; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00331serine/threonine kinase 11approvedMetformin


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Cross referenced IDs for STK11
* 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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