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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for AFMID |
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Phenotypic Information for AFMID(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: AFMID |
Familial Cancer Database: AFMID |
* 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/ |
Metabolic Pathway Description | |
KEGG_TRYPTOPHAN_METABOLISM KEGG_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: AFMID |
MedGen: AFMID (Human Medical Genetics with Condition) | |
ClinVar: AFMID | |
Phenotype | MGI: AFMID (International Mouse Phenotyping Consortium) |
PhenomicDB: AFMID |
Mutations for AFMID |
* 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 |
- Statistics for Tissue and Mutation type | Top |
- For Inter-chromosomal Variations |
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'. |
- 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'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | AFMID | chr17 | 76187407 | 76187427 | AFMID | chr17 | 76188778 | 76188798 |
pancreas | AFMID | chr17 | 76188972 | 76188992 | AFMID | chr17 | 76193485 | 76193505 |
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) |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows AFMID 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 |
W90454 | A2M | 1 | 284 | 12 | 9243915 | 9247627 | AFMID | 278 | 411 | 17 | 76203648 | 76203780 | |
BX509939 | IDS | 1 | 290 | X | 148560307 | 148560595 | AFMID | 276 | 671 | 17 | 76202062 | 76203316 | |
BX647783 | AFMID | 2 | 644 | 17 | 76183443 | 76203316 | IDS | 630 | 925 | X | 148560300 | 148560595 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
GAIN (# sample) | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
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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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=26) | (# total SNVs=7) |
(# total SNVs=0) | (# total SNVs=0) |
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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 |
chr17:76201787-76201787 | p.E250K | 3 |
chr17:76201792-76201792 | p.F251F | 3 |
chr17:76200772-76200772 | p.T115M | 2 |
chr17:76187059-76187059 | p.E24D | 2 |
chr17:76187085-76187085 | p.V33A | 2 |
chr17:76201534-76201534 | p.V193V | 2 |
chr17:76201678-76201678 | p.? | 2 |
chr17:76201688-76201688 | p.D217Y | 1 |
chr17:76198600-76198600 | p.T59S | 1 |
chr17:76201796-76201796 | p.R253* | 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 | 2 | 1 |   | 5 |   |   | 2 |   | 1 |   |   | 5 |   | 1 |   |   | 7 | 1 |   | 5 |
# mutation | 2 | 1 |   | 5 |   |   | 2 |   | 1 |   |   | 5 |   | 1 |   |   | 5 | 1 |   | 6 |
nonsynonymous SNV | 2 | 1 |   | 3 |   |   | 2 |   | 1 |   |   | 3 |   | 1 |   |   | 3 | 1 |   | 4 |
synonymous SNV |   |   |   | 2 |   |   |   |   |   |   |   | 2 |   |   |   |   | 2 |   |   | 2 |
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 |
chr17:76201792 | p.F251F,AFMID | 3 |
chr17:76200772 | p.T115M,AFMID | 2 |
chr17:76187059 | p.E24D,AFMID | 2 |
chr17:76201707 | p.A108A,AFMID | 1 |
chr17:76198676 | p.Q303H,AFMID | 1 |
chr17:76201752 | p.Y152C,AFMID | 1 |
chr17:76200751 | p.G195V,AFMID | 1 |
chr17:76201777 | p.L215M,AFMID | 1 |
chr17:76200752 | p.D217Y,AFMID | 1 |
chr17:76201782 | p.D3N,AFMID | 1 |
Other DBs for Point Mutations |
Copy Number for AFMID 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 AFMID |
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 |
AFMID,AKR1C2,AKR1D1,C15orf43,CLPSL1,C6orf223,ARMC12, CDC42EP5,DBI,GGT1,GGT3P,GGTLC1,GGTLC2,HPD, KCNG2,LOC644165,RRP7B,SERHL2,SERHL,SPINK8,SULT1C3 | ABCC11,AFMID,ALOX15B,B3GAT1,C15orf43,C6orf223,DHRS2, GGT1,HMGCS2,HPGD,HSD3B2,LST-3TM12,MPV17L,NSUN2, PNLIPRP3,SERHL2,SERHL,SRD5A1,TARP,TMPRSS11F,UGT2B10 | ||||
AFMID,ANAPC11,AUP1,TEN1,C17orf89,DCXR,EIF1, GPS1,ICT1,MRPL12,MRPL38,MRPS7,NARF,NAT9, NME2,NT5C3B,PHB,RPL38,SUMO2,TMEM101,TSEN54 | AFMID,BID,C12orf66,FOPNL,EIF4EBP1,GEMIN7,GSTO2, KRTCAP3,NIPSNAP1,RPL18A,RPL29,RPLP0,SFXN4,SUMF2, SYNGR2,TARBP2,TBCCD1,TBL2,TGIF1,TMEM5,YIPF2 |
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 AFMID |
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 |
DB00130 | arylformamidase | approved; nutraceutical; investigational | L-Glutamine | ||
DB00160 | arylformamidase | approved; nutraceutical | L-Alanine | ||
DB00150 | arylformamidase | approved; nutraceutical | L-Tryptophan |
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Cross referenced IDs for AFMID |
* 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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