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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SACM1L |
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Phenotypic Information for SACM1L(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: SACM1L |
Familial Cancer Database: SACM1L |
* 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/ |
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REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_PI_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: SACM1L |
MedGen: SACM1L (Human Medical Genetics with Condition) | |
ClinVar: SACM1L | |
Phenotype | MGI: SACM1L (International Mouse Phenotyping Consortium) |
PhenomicDB: SACM1L |
Mutations for SACM1L |
* 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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- Statistics for Tissue and Mutation type | Top |
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- 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'. |
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Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
pancreas | SACM1L | chr3 | 45741653 | 45741673 | chr3 | 66957780 | 66957800 | |
pancreas | SACM1L | chr3 | 45768351 | 45768371 | SACM1L | chr3 | 45768667 | 45768687 |
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) |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SACM1L 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 |
DA761308 | WDR43 | 1 | 78 | 2 | 29136536 | 29136613 | SACM1L | 79 | 520 | 3 | 45730927 | 45751067 | |
CB410891 | LINC00478 | 1 | 444 | 21 | 17623955 | 17624398 | SACM1L | 440 | 528 | 3 | 45786080 | 45786168 | |
CA949726 | SACM1L | 1 | 91 | 3 | 45781107 | 45785085 | SACM1L | 87 | 548 | 3 | 45785077 | 45785538 |
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Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample | 3 |   |   | 2 |   |   | 1 |   |   |   | 1 |   |   | 2 |   |   | 1 | |||
GAIN (# sample) | 3 |   |   | 2 |   |   | 1 |   |   |   | 1 |   |   | 1 |   |   | 1 | |||
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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Stat. for Non-Synonymous SNVs (# total SNVs=33) | (# total SNVs=8) |
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(# total SNVs=0) | (# 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 |
chr3:45780149-45780149 | p.D488N | 5 |
chr3:45779136-45779136 | p.Y434F | 3 |
chr3:45751048-45751048 | p.F131S | 2 |
chr3:45780132-45780132 | p.Y482C | 2 |
chr3:45746676-45746676 | p.I60M | 2 |
chr3:45776753-45776753 | p.Q376R | 1 |
chr3:45780151-45780151 | p.D488D | 1 |
chr3:45748362-45748362 | p.S99F | 1 |
chr3:45754685-45754685 | p.P180P | 1 |
chr3:45785052-45785052 | p.Y552F | 1 |
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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 | 1 | 1 |   | 7 |   |   | 3 |   | 1 | 2 |   | 1 | 2 | 1 |   | 2 | 1 | 5 |   | 2 |
# mutation | 1 | 1 |   | 7 |   |   | 3 |   | 1 | 2 |   | 3 | 2 | 1 |   | 2 | 1 | 5 |   | 2 |
nonsynonymous SNV | 1 | 1 |   | 4 |   |   | 1 |   |   | 2 |   | 3 | 2 |   |   | 1 |   | 3 |   | 1 |
synonymous SNV |   |   |   | 3 |   |   | 2 |   | 1 |   |   |   |   | 1 |   | 1 | 1 | 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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* 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 |
chr3:45751048 | p.F131S | 2 |
chr3:45745000 | p.R35S | 2 |
chr3:45761023 | p.D488D | 1 |
chr3:45781107 | p.H65N | 1 |
chr3:45746631 | p.D493N | 1 |
chr3:45773624 | p.K102K | 1 |
chr3:45785048 | p.P512H | 1 |
chr3:45746689 | p.I110I | 1 |
chr3:45773632 | p.A523V | 1 |
chr3:45785050 | p.V125V | 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 SACM1L |
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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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ACTR8,APPL1,AZI2,FAM208A,CLASP2,DCP1A,DENND6A, KIAA1143,LZTFL1,NEK4,PBRM1,PDCD6IP,PDE12,QRICH1, SACM1L,SETD2,SLMAP,TMF1,VPRBP,ZNF197,ZNF621 | AP3M1,CDC73,DCUN1D4,ERI1,EXOC1,FAM172A,GDAP2, GNAQ,LUZP6,NAB1,OSBPL8,SACM1L,SLC30A5,SMAD2, SMEK2,TBC1D23,TMEM167A,TMX3,USP33,VAMP4,VPS41 |
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TCAIM,C3orf38,TRAPPC13,CAPN7,CRBN,DPH3,EIF1B, HIGD1A,LYRM7,LZTFL1,MKRN2,OXNAD1,PCNP,PDCD10, PDHB,RPP14,SACM1L,SELT,SPCS1,UBA3,ZCCHC10 | ARFIP1,SMIM15,CAAP1,CD46,MICU2,FPGT,GMFB, KRCC1,LYSMD3,NRAS,PEX13,RFWD2,SACM1L,SFT2D1, SGK3,SLMO2,SNX14,TMED5,TMEM167A,VTA1,ZCCHC10 |
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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 SACM1L |
There's no related Drug. |
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Cross referenced IDs for SACM1L |
* 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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