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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for LDHC |
Basic gene info. | Gene symbol | LDHC |
Gene name | lactate dehydrogenase C | |
Synonyms | CT32|LDH3|LDHX | |
Cytomap | UCSC genome browser: 11p15.1 | |
Genomic location | chr11 :18433852-18472793 | |
Type of gene | protein-coding | |
RefGenes | NM_002301.4, NM_017448.3, | |
Ensembl id | ENSG00000166796 | |
Description | L-lactate dehydrogenase C chainLDH testis subunitLDH-CLDH-Xcancer/testis antigen 32lactate dehydrogenase C4lactate dehydrogenase c variant 1lactate dehydrogenase c variant 3lactate dehydrogenase c variant 4 | |
Modification date | 20141207 | |
dbXrefs | MIM : 150150 | |
HGNC : HGNC | ||
Ensembl : ENSG00000166796 | ||
HPRD : 01027 | ||
Vega : OTTHUMG00000167722 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_LDHC | |
BioGPS: 3948 | ||
Gene Expression Atlas: ENSG00000166796 | ||
The Human Protein Atlas: ENSG00000166796 | ||
Pathway | NCI Pathway Interaction Database: LDHC | |
KEGG: LDHC | ||
REACTOME: LDHC | ||
ConsensusPathDB | ||
Pathway Commons: LDHC | ||
Metabolism | MetaCyc: LDHC | |
HUMANCyc: LDHC | ||
Regulation | Ensembl's Regulation: ENSG00000166796 | |
miRBase: chr11 :18,433,852-18,472,793 | ||
TargetScan: NM_002301 | ||
cisRED: ENSG00000166796 | ||
Context | iHOP: LDHC | |
cancer metabolism search in PubMed: LDHC | ||
UCL Cancer Institute: LDHC | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for LDHC(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: LDHC |
Familial Cancer Database: LDHC |
* This gene is included in those cancer gene databases. |
Oncogene 1 | Significant driver gene in |
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/ |
Metabolic Pathway Description | |
KEGG_GLYCOLYSIS_GLUCONEOGENESIS KEGG_CYSTEINE_AND_METHIONINE_METABOLISM KEGG_PYRUVATE_METABOLISM KEGG_PROPANOATE_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: LDHC |
MedGen: LDHC (Human Medical Genetics with Condition) | |
ClinVar: LDHC | |
Phenotype | MGI: LDHC (International Mouse Phenotyping Consortium) |
PhenomicDB: LDHC |
Mutations for LDHC |
* 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows LDHC related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
BU569321 | RGS22 | 8 | 463 | 8 | 100990196 | 100999854 | LDHC | 458 | 600 | 11 | 18472647 | 18472789 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=30) | (# total SNVs=5) |
(# total SNVs=0) | (# total SNVs=2) |
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Top 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 position | Mutation(aa) | Unique sampleID count |
chr11:18456337-18456337 | p.R157C | 2 |
chr11:18460142-18460142 | p.T220T | 2 |
chr11:18472565-18472565 | p.R297Q | 2 |
chr11:18451403-18451403 | p.P122S | 2 |
chr11:18436817-18436817 | p.F71L | 2 |
chr11:18451302-18451302 | p.N88S | 1 |
chr11:18472540-18472540 | p.L289I | 1 |
chr11:18434294-18434294 | p.E10E | 1 |
chr11:18460141-18460141 | p.T220M | 1 |
chr11:18451306-18451306 | p.S89S | 1 |
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SNV Counts per Each Loci in TCGA data |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 3 | 2 |   | 4 |   |   | 3 |   | 1 |   |   | 8 | 3 | 1 |   |   | 7 | 1 |   | 4 |
# mutation | 3 | 2 |   | 4 |   |   | 3 |   | 1 |   |   | 9 | 3 | 1 |   |   | 6 | 1 |   | 5 |
nonsynonymous SNV |   | 2 |   | 3 |   |   | 2 |   | 1 |   |   | 7 | 3 | 1 |   |   | 4 | 1 |   | 4 |
synonymous SNV | 3 |   |   | 1 |   |   | 1 |   |   |   |   | 2 |   |   |   |   | 2 |   |   | 1 |
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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Top 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 Position | Mutation(aa) | Unique sampleID count |
chr11:18456337 | p.R157C,LDHC | 3 |
chr11:18451302 | p.E6Q,LDHC | 1 |
chr11:18456442 | p.S151G,LDHC | 1 |
chr11:18434294 | p.R297Q,LDHC | 1 |
chr11:18472604 | p.E10E,LDHC | 1 |
chr11:18451306 | p.S310F,LDHC | 1 |
chr11:18460094 | p.L12L,LDHC | 1 |
chr11:18434300 | p.A168G,LDHC | 1 |
chr11:18472617 | p.A314A,LDHC | 1 |
chr11:18451362 | p.N18K,LDHC | 1 |
Other DBs for Point Mutations |
Copy Number for LDHC 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 LDHC |
Gene 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. |
Differential 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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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-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 |
ARHGEF33,BCL11A,BEND4,MCMBP,LINC01553,HENMT1,MMS22L, C7orf66,CTXN3,EDAR,FAM81A,FLJ36000,GPR156,KIAA1841, LDHC,LGR6,PGLYRP1,PRKD3,SGOL1,SLC16A10,TTK | ANKRD20A3,BAGE,DSTN,FAM133A,ZC2HC1A,TVP23C,GKN1, GRPR,IFNA17,LDHC,LAMTOR3,NPTN,PCNP,PEX2, SLC16A9,STK3,TERF1,TMEM128,TMEM68,VMA21,ZFAND1 | ||||
ACSBG2,C2orf48,CYP2A6,FAM122B,GOLGA6L1,GOLGA6L6,GOLGA8CP, GPR19,LDHC,LOC100303728,LOC144486,LOC400752,LOC401588,LOC645752, NAE1,PDYN,RAD51AP1,RPA3,SLC4A9,TMEM116,TMEM194A | ALOX15B,ANTXRL,ATXN3,C15orf43,C7orf13,CA5A,CCDC122, EVX1,FRRS1,ITGA10,LDHC,LINC01512,MC3R,MOBP, OR10J3,OR1L6,RRM2B,SNORA24,ZBTB44,ZNF33B,ZNF543 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for LDHC |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00157 | lactate dehydrogenase C | approved; nutraceutical | NADH |
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Cross referenced IDs for LDHC |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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