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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SEMA6D |
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Phenotypic Information for SEMA6D(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: SEMA6D |
Familial Cancer Database: SEMA6D |
* This gene is included in those cancer gene databases. |
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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/ |
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REACTOME_METABOLISM_OF_PROTEINS |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: SEMA6D |
MedGen: SEMA6D (Human Medical Genetics with Condition) | |
ClinVar: SEMA6D | |
Phenotype | MGI: SEMA6D (International Mouse Phenotyping Consortium) |
PhenomicDB: SEMA6D |
Mutations for SEMA6D |
* 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. |
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There's no structural variation information in COSMIC data for this gene. |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SEMA6D 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 |
DA213399 | HPCAL1 | 1 | 150 | 2 | 10500837 | 10500986 | SEMA6D | 148 | 558 | 15 | 48060775 | 48062933 |
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There's no copy number variation information in COSMIC data for this gene. |
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Stat. for Non-Synonymous SNVs (# total SNVs=137) | (# total SNVs=48) |
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(# total SNVs=1) | (# total SNVs=0) |
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* 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 |
chr15:48062707-48062707 | p.E649D | 5 |
chr15:48063628-48063628 | p.T956T | 4 |
chr15:48063126-48063126 | p.K789R | 3 |
chr15:48062764-48062764 | p.V668V | 3 |
chr15:48056425-48056425 | p.F340L | 3 |
chr15:48063190-48063190 | p.P810P | 3 |
chr15:48053907-48053907 | p.C166Y | 3 |
chr15:48062819-48062819 | p.R687R | 3 |
chr15:48057216-48057216 | p.V464I | 3 |
chr15:48053596-48053596 | p.N139D | 3 |
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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 | 5 | 2 | 2 | 16 | 2 |   | 8 |   | 5 |   | 1 | 29 | 11 |   |   | 1 | 6 | 20 |   | 19 |
# mutation | 5 | 2 | 2 | 17 | 2 |   | 8 |   | 5 |   | 1 | 33 | 12 |   |   | 1 | 6 | 22 |   | 31 |
nonsynonymous SNV | 4 | 1 | 1 | 14 | 1 |   | 4 |   | 3 |   | 1 | 27 | 11 |   |   | 1 | 3 | 15 |   | 21 |
synonymous SNV | 1 | 1 | 1 | 3 | 1 |   | 4 |   | 2 |   |   | 6 | 1 |   |   |   | 3 | 7 |   | 10 |
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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* 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 |
chr15:48056400 | p.S332N,SEMA6D | 3 |
chr15:48062707 | p.E587D,SEMA6D | 3 |
chr15:48060877 | p.C515C,SEMA6D | 2 |
chr15:48063573 | p.S852S,SEMA6D | 2 |
chr15:48063880 | p.T978T,SEMA6D | 2 |
chr15:48058183 | p.R876I,SEMA6D | 2 |
chr15:48056121 | p.G325G,SEMA6D | 2 |
chr15:48056380 | p.R622Q | 2 |
chr15:48063502 | p.W274C,SEMA6D | 2 |
chr15:48063266 | p.D408N,SEMA6D | 1 |
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* 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. |
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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 SEMA6D |
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* 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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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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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APLP1,CACNA2D3,DKFZP434H168,DYTN,FLJ46111,GNAO1,GRIA1, HAO2,KRTAP19-2,KRTAP25-1,KRTAP6-1,OR5D18,PCSK1,PPP1R1C, PTPRN,RTBDN,RUNDC3A,SEMA6D,TAGLN3,TPH2,TWISTNB | B3GALT1,COLCA1,CBFA2T2,EDAR,GPR144,IL17RD,KCNJ13, KIF5A,LCA5,LZTS1,NEO1,RARB,RASSF6,SCN2A, SEMA6D,ST8SIA2,TRIM9,ZMYM3,ZKSCAN7,ZNF648,ZNF827 |
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BMP3,CA4,CDKN2B-AS1,CEACAM7,CHP2,TMEM236,GNA11, GPR15,HTR4,MS4A12,SLC51B,PHLPP2,SEMA6D,SLC25A34, SLC26A3,SLC30A10,TMEM37,TMIGD1,TRIM40,XDH,ZZEF1 | ACSL5,ARAP2,C18orf8,MISP,CARD10,DAPK2,ERBB2IP, GK,GNA11,GPR128,HKDC1,IL32,KIAA0247,LASP1, LRRC66,MOV10,PLS1,PTPRJ,RAB8A,SEMA6D,SLC9A3R1 |
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* 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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Pharmacological Information for SEMA6D |
There's no related Drug. |
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Cross referenced IDs for SEMA6D |
* 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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