|
Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for GEMIN6 |
Basic gene info. | Gene symbol | GEMIN6 |
Gene name | gem (nuclear organelle) associated protein 6 | |
Synonyms | - | |
Cytomap | UCSC genome browser: 2p22.1 | |
Genomic location | chr2 :39005326-39009106 | |
Type of gene | protein-coding | |
RefGenes | NM_024775.9, | |
Ensembl id | ENSG00000152147 | |
Description | SIP2gem-associated protein 6gemin 6gemin-6 | |
Modification date | 20141207 | |
dbXrefs | MIM : 607006 | |
HGNC : HGNC | ||
HPRD : 06110 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_GEMIN6 | |
BioGPS: 79833 | ||
Gene Expression Atlas: ENSG00000152147 | ||
The Human Protein Atlas: ENSG00000152147 | ||
Pathway | NCI Pathway Interaction Database: GEMIN6 | |
KEGG: GEMIN6 | ||
REACTOME: GEMIN6 | ||
ConsensusPathDB | ||
Pathway Commons: GEMIN6 | ||
Metabolism | MetaCyc: GEMIN6 | |
HUMANCyc: GEMIN6 | ||
Regulation | Ensembl's Regulation: ENSG00000152147 | |
miRBase: chr2 :39,005,326-39,009,106 | ||
TargetScan: NM_024775 | ||
cisRED: ENSG00000152147 | ||
Context | iHOP: GEMIN6 | |
cancer metabolism search in PubMed: GEMIN6 | ||
UCL Cancer Institute: GEMIN6 | ||
Assigned class in ccmGDB | C |
Top |
Phenotypic Information for GEMIN6(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: GEMIN6 |
Familial Cancer Database: GEMIN6 |
* 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 | |
REACTOME_METABOLISM_OF_NON_CODING_RNA REACTOME_METABOLISM_OF_RNA |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: GEMIN6 |
MedGen: GEMIN6 (Human Medical Genetics with Condition) | |
ClinVar: GEMIN6 | |
Phenotype | MGI: GEMIN6 (International Mouse Phenotyping Consortium) |
PhenomicDB: GEMIN6 |
Mutations for GEMIN6 |
* 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 GEMIN6 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 |
Other DBs for Structural Variants |
Top |
Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
Top |
SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
|
Top |
Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=14) | (# total SNVs=3) |
(# total SNVs=0) | (# total SNVs=0) |
Top |
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 |
chr2:39008760-39008760 | p.R77T | 1 |
chr2:39008997-39008997 | p.Q156R | 1 |
chr2:39008778-39008778 | p.M83K | 1 |
chr2:39009027-39009027 | p.S166F | 1 |
chr2:39008788-39008788 | p.F86F | 1 |
chr2:39008826-39008826 | p.L99Q | 1 |
chr2:39008833-39008833 | p.E101E | 1 |
chr2:39006139-39006139 | p.E3* | 1 |
chr2:39008851-39008851 | p.K107N | 1 |
chr2:39006172-39006172 | p.D14Y | 1 |
Top |
SNV Counts per Each Loci in TCGA data |
|
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 |   |   |   |   | 1 |   |   |   |   |   |   |   | 1 |   |   | 1 |
# mutation |   |   |   | 4 |   |   |   |   | 1 |   |   |   |   |   |   |   | 1 |   |   | 1 |
nonsynonymous SNV |   |   |   | 4 |   |   |   |   |   |   |   |   |   |   |   |   | 1 |   |   | 1 |
synonymous SNV |   |   |   |   |   |   |   |   | 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]) |
Top |
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 |
chr2:39008997 | p.D14Y | 1 |
chr2:39009027 | p.G59R | 1 |
chr2:39006172 | p.M61V | 1 |
chr2:39008705 | p.K107N | 1 |
chr2:39008711 | p.T134T | 1 |
chr2:39008851 | p.I150S | 1 |
chr2:39008932 | p.Q156R | 1 |
chr2:39008979 | p.S166F | 1 |
Other DBs for Point Mutations |
Copy Number for GEMIN6 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] |
Top |
Gene Expression for GEMIN6 |
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)) |
Top |
CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
Top |
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 |
AUP1,BOLA3,C17orf89,C19orf53,COX7B,DGUOK,DPY30, EIF5A,GEMIN6,KRTCAP2,MORN2,MPV17,MRPL17,MRPS15, NDUFA1,OST4,PFDN6,PPM1G,SHFM1,SNRPG,TIMM8B | APOA1BP,EIF3I,FIBP,GEMIN6,LOC152217,LSM2,MEA1, MRFAP1,MRPL17,MRPL51,MRPS21,NABP2,PFDN5,POLR2G, PPIA,SMUG1,SNRPF,TIMM22,TMEM223,TOMM22,UFC1 |
BOLA3,C19orf53,C8orf59,CCDC58,DPY30,GEMIN6,HSPE1, MEMO1,METTL5,NIFK,MRPL40,MRPS23,NME1,POLR2F, RPL26L1,SF3B14,SNRPG,SS18L2,SSBP1,SUMO1,TPRKB | ELP6,COMMD10,CWC15,DRG1,GEMIN6,HAX1,ICT1, LSM2,MED31,MRPS15,MRPS23,NDUFA4,NUP54,POLE3, PRDX3,PSMD10,SNRPD2,THOC7,TMEM126A,TMEM126B,TOMM6 |
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 |
Top |
Interacting Genes (from Pathway Commons) |
Top |
Pharmacological Information for GEMIN6 |
There's no related Drug. |
Top |
Cross referenced IDs for GEMIN6 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @ |